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PREP Publications Piscataqua Region Estuaries Partnership

2000

A Technical Characterization of Estuarine andCoastal New HampshireNew Hampshire Estuaries Project

Stephen H. JonesUniversity of New Hampshire

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Recommended CitationNew Hampshire Estuaries Project and Jones, Stephen H., "A Technical Characterization of Estuarine and Coastal New Hampshire"(2000). PREP Publications. Paper 294.http://scholars.unh.edu/prep/294

AR-293

A Technical Characterization of

Estuarine and Coastal New Hampshire

Published by the New Hampshire Estuaries Project

Edited by Dr. Stephen H. Jones

Jackson estuarine Laboratory, university of New Hampshire Durham, NH

2000

i

ACKNOWLEDGEMENTS

TABLE OF CONTENTS ............................................................................................i

LIST OF TABLES ....................................................................................................vi

LIST OF FIGURES.................................................................................................viii

PREFACE ..............................................................................................................xii

EXECUTIVE SUMMARY........................................................................................xiii

CHAPTER 1 INTRODUCTION .........................................................................1

1.1 Geographical and Physical Settings. ..........................................................41.1.1 The Great Bay Estuary ..........................................................................41.1.2 Hampton Harbor Estuary......................................................................81.1.3 Beach and Dune Systems .....................................................................9

1.2 Biological Setting......................................................................................101.2.1 Fish and Shellfish................................................................................101.2.2 Birds and Mammals............................................................................111.2.3 Primary Producers ..............................................................................12

1.3 Human Setting..........................................................................................131.3.1 Recreational Resources and Values ......................................................13

1.3.1.1 Boating ......................................................................................141.3.1.2 Shellfishing.................................................................................141.3.1.3 Fishing .......................................................................................141.3.1.4 Passive Recreation ......................................................................18

1.3.2 Commercial Resources and Values ......................................................191.3.2.1 Industry and shipping ................................................................191.3.2.2 Fishing .......................................................................................191.3.2.3 Tourism and Recreational Industries ...........................................19

CHAPTER 2 PRESENT AND HISTORICAL STATUS AND TRENDS OF WATER QUALITY ............................21

2.1 Overall Water Quality and Use Support...................................................222.1.1 Background........................................................................................222.1.2 Status and Trends of Overall Water Quality and Use Support .............24

2.2 Status and Trends of Microbial Pathogens and Fecal Indicators ............272.2.1 Pathogens, Bacterial Fecal Indicators, and Water Quality Standards....27

2.2.1.1 Spatial Distribution.....................................................................28Great Bay and Upper Little Bay with the

Squamscott/Exeter and Lamprey Rivers .................................28Oyster and Bellamy rivers and Lower Little Bay ..........................33Salmon Falls, Cocheco and (Upper) Piscataqua Rivers ................35Portsmouth and Little Harbors and Lower Piscataqua River ........37Rye Harbor and Coastline...........................................................38Hampton Harbor and Tributaries................................................39

2.2.1.2 Temporal Trends ........................................................................40

TABLE OF CONTENTS

2.2.2 Sources of Fecal-Borne Microorganisms..............................................442.2.2.1 Storm-related Runoff..................................................................452.2.2.2 Wastewater Treatment Facilities and

Combined Sewer Overflows...................................................472.2.2.3 Septic Systems ...........................................................................502.2.2.4 Agricultural Runoff and Other Nonpoint Sources .......................51

2.2.3. Modeling and Dye Studies for Bacterial Fate and Transport................522.2.4 Impacts of Fecal-Borne Bacteria on Shellfishing ..................................53

2.2.4.1 Historical Sanitary Assessments of Shellfish-growing Waters .......532.2.4.2 Present Conditions .....................................................................57

2.2.5 Impacts of Microbial Contamination ..................................................582.2.6 Fecal-Borne Viruses and Historical Studies on

Indicators and Pathogens ..........................................................582.2.7 Autochthonous Microbial Pathogens ..................................................60

2.3 Toxic Organic and Metal Contaminants ..................................................622.3.1 Status and Trends for Contaminants in Water.....................................622.3.2 Status and Trends for Contaminated Sediments. ................................632.3.3 Sources of Toxic Contaminants...........................................................70

2.3.3.1 Stormwater Runoff .....................................................................702.3.3.2 Superfund Sites ..........................................................................712.3.3.3 Documented Groundwater Pollution Sources.............................732.3.3.4 Oil Spills.....................................................................................772.3.3.5 Fertilizer and Pesticide Applications............................................782.3.3.6 Atmospheric Deposition.............................................................792.3.3.7 Summary ...................................................................................79

2.3.4 Contaminant and Hydrodynamic Modelling.......................................802.3.5 Public Health Risks and Ecological Impacts. ........................................81

2.4 Inorganic and Organic Nutrients .............................................................872.4.1 Nutrient Conditions in New Hampshire’s Estuaries. ............................872.4.2 Trends in Nutrient Concentrations......................................................922.4.3. Relationship to Water Quality Standards.............................................952.4.4 Pollution Sources and Nitrogen Loading Estimates. ............................962.4.5 Documented Impacts on Water Chemistry and Natural Resources ...101

2.4.5.1 Dissolved Oxygen. ...................................................................1022.4.5.2 Phytoplankton Blooms .............................................................1052.4.5.3 Eutrophication. ........................................................................107

2.5 Suspended Sediments and Turbidity......................................................1092.5.1 Surficial Sediments Around Great Bay Estuary ..................................1092.5.2 Shoreline Characteristics in the Great Bay Estuary ............................1092.5.3 Sources of Sediments .......................................................................1102.5.4 Suspended Sediments ......................................................................1102.5.5 Sedimentation Processes on Great Bay Tidal Flats.............................113

2.6 Other Contaminants of Potential Concern ............................................1142.6.1 Radionuclides ...................................................................................1142.6.2 Biotoxins ..........................................................................................1142.6.3 Acid Rain ..........................................................................................1152.6.4 Marine Debris...................................................................................1152.6.5 Other Contaminants.........................................................................116

2.7 Summary of Findings ..............................................................................117ii

iii

CHAPTER 3 LIVING RESOURCES................................................................121

3.1 Estuarine Invertebrates...........................................................................1223.1.1 Zooplankton.....................................................................................1223.1.2 Benthic Invertebrates........................................................................1233.1.3 Selected Invertebrate Species ...........................................................124

3.1.3.1 Molluscan Shellfish...................................................................124Eastern Oyster (Crassostrea virginica) ....................................125Diseases of the Eastern Oyster in New Hampshire................128Belon or European Flat Oyster (Ostrea edulis) ......................130Softshell Clam (Mya arenaria) ..............................................130Blue Mussel (Mytilus edulis). .................................................137Sea Scallops (Placopecten magellanicus) ................................138Other Bivalve Species...........................................................138

3.1.3.2 Crustaceans..............................................................................139American Lobster (Homarus americanus) ..............................139Crabs ...................................................................................139Horseshoe Crabs (Limulus polyphemus).................................139

3.2 Estuarine Finfish ......................................................................................1403.2.1 Selected Species ...............................................................................140

3.2.1.1 Striped Bass (Morone saxatilis) ..................................................1403.2.1.2 Winter Flounder (Pleuronectes americanus) ...............................1423.2.1.3 Rainbow Smelt (Osmerus mordax) ............................................1423.2.1.4 River Herring (Alosa pseudoharengus and Alosa aestevalis) ........1433.2.1.5 American Shad (Alosa sapidissima) ...........................................1433.2.1.6 Atlantic Silversides (Menidia menidia) .......................................1443.2.1.7 Atlantic Salmon (Salmo salar) ...................................................144

3.2.2 Fish Kills ...........................................................................................146

3.3 Marine Plant Habitats: Salt Marshes, Macroalgal Beds, and Eelgrass Meadows .......................147

3.3.1 Status and Trends of Saltmarsh.........................................................1473.3.1.1 Distribution, Standing Crop and Productivity...........................1473.3.1.2 Habitat Impacts and Losses .....................................................148

Dredging Impacts and Harvesting Effects.............................148Impacts from Docks, Piers and Shoreline Development ......150Impacts from Tidal Restrictions ...........................................150

3.3.1.3 Habitat Change Analysis and Modeling ..................................1513.3.2 Status and Trends of Macroalgae......................................................152

3.3.2.1 Distribution, Standing Crop and Productivity ..........................1523.3.2.2 Habitat Impacts and Losses ......................................................1533.3.2.3 Habitat Change Analysis and Modeling ..................................155

3.3.3 Status and Trends of Eelgrass Beds ...................................................1553.3.3.1 Distribution, Standing Crop and Productivity ..........................1553.3.3.2 Habitat Impacts and Losses ......................................................156

Dredging Impacts on Benthic Habitats and Sediments ........157Impacts from Boating, Docks and Piers................................157Impacts from Shoreline Development and Harvesting .........157

3.3.3.3 Habitat Change Analysis and Modeling ..................................158

3.4 Wildlife ............................................................................................1613.4.1 Marine Mammals ............................................................................1613.4.2 Waterfowl and Shorebirds ................................................................1613.4.3 Non-Game Species...........................................................................1623.4.4 Rare and Endangered Species...........................................................163

3.5 Introduced and Nuisance Species ..........................................................1643.5.1 Green Crabs (Carcinus maenas): Introduced and Nuisance. ..............1643.5.2 European Oyster (Ostrea edulis): Introduced. ....................................1643.5.3 Common Periwinkle (Littorina littorea): Introduced...........................1643.5.4 Oyster Drill (Urosalpinx cinerea): Nuisance .......................................1643.5.5 Sea Lettuce (Ulva latuca): Nuisance ..................................................1653.5.6 Other Introduced and Nuisance Plant Species .................................165

3.6 Summary of Findings .............................................................................166

CHAPTER 4 HUMAN USES AND RESOURCE MANAGEMENT ..................169

4.1 Population Trends, Employment and Income ......................................1704.1.1 Population and Density Trends and Projections ...............................1704.1.2 Employment and Income ................................................................171

4.2 Land Use and Development Issues ........................................................1724.2.1 Urban and Rural Development .........................................................1724.2.2 Estuarine Shoreland..........................................................................1744.2.3 Habitat Loss and Fragmentation ......................................................174

4.3 Estuarine and Marine Uses and Issues ..................................................1754.3.1 Commercial Uses .............................................................................175

4.3.1.1 Shipping and Commercial Vessel Traffic ...................................1754.3.1.2 Dredge and Disposal................................................................1764.3.1.3 Commercial Fisheries and Aquaculture.....................................177

Lobsters ...............................................................................177Other Commercial Fisheries .................................................182Aquaculture .........................................................................184

4.3.1.4 Marine Products.......................................................................1854.3.1.5 Marine Plant Harvesting...........................................................185

4.3.2 Recreational Uses..............................................................................1854.3.2.1 Tourism Economics ..................................................................1854.3.2.2 Boating and Related Activities ..................................................1864.3.2.3 Recreational Fishing .................................................................1874.3.2.4 Shellfish Resource Management and Recreational Harvesting...189

Effects of Classification on Shellfish Resource Productivity ....189Harvesting Effects on Other Wildlife.....................................190Siltation and Harvesting Effects ...........................................191Management Strategies for Recreational Beds and Flats.......192Illegal Harvesting .................................................................192Post-harvest Processing........................................................192

4.4 Managing Human Uses ............................................................................1934.4.1 Base Program Analysis ......................................................................1934.4.2 Land Protection ...............................................................................1934.4.3 Habitat Restoration and Mitigation ..................................................194

4.4.3.1 Anadromous Fish Restoration ...................................................1944.4.3.2 Shellfish Restoration .................................................................1944.4.3.3 Saltmarsh Restoration .............................................................1974.4.3.4 Eelgrass Restoration..................................................................198

4.3.5 Port of New Hampshire Mitigation ......................................................198

4.5 Summary of Findings ...............................................................................200iv

v

CHAPTER 5 SUMMARY OF FINDINGS...................................................201

CHAPTER 6 BIBLIOGRAPHY ..................................................................209

APPENDICES

Appendix A Population and Population Density of Rockingham and Strafford County Towns ....................................................239

Appendix B Drainage Area and Discharge of Tributaries to the Great Bay Estuary.....................................................................241

Appendix C Land Cover and Land Use Classification and Areas for the Great Bay and Hampton Harbor Estuary Watersheds..........243

Appendix D Abundance and Value of New Hampshire Shellfish Resources ...................................................................245

Appendix E Finfish and Intertidal and Subtidal Infaunal Invertebrate Species in the Great Bay Estuary ..............................................247

Appendix F Status and Trends for Overall Quality and Use Support for Water Quality in New Hampshire’s Coastal Surface Waters: 1988-1996. .....................................................249

Appendix G Fecal Coliform Data for Great Bay, Little Harbor, Rye Harbor and Hampton Harbor: 1985-1996 .........................251

Appendix H Tissue Concentrations of Toxic Contaminants in Bivalve Shellfish, Lobsters, Winter Flounder and Marine Plants.............255

Appendix I Zooplankton Species in the Great Bay Estuary..........................265

Appendix J Species of Seaweeds and Plants Occurring in New Hampshire Salt Marshes ...........................................................267

Appendix K Threatened and Endangered Animal and Plant Species in Great Bay.................................................................273

xv

This technical characterization reportprovides a comprehensive compila-

tion of information on key issues relatedto water quality and natural resources inthe estuaries of New Hampshire. Thereport has identified some significantissues and problems facing these estuar-ies that will require management atten-tion. Issues common to estuaries acrossthe nation have been addressed to vary-ing extents, depending on their signifi-cance in New Hampshire. Much of thetrend information is biased by the spo-radic interest given to the differentresources and water quality issuesthrough the years. Studies have focusedto differing extents on the various areasof the coast, providing more informationand better documentation where greaterscrutiny was given. Problems have beenidentified in relation to accepted stan-dards where possible to provide thebasis for developing a clearer vision forthe future of New Hampshire’s coastalresources and water quality.

Bacterial contamination of estuarinewaters in New Hampshire is widespread.There are no grossly contaminated areas,but every estuarine surface water body issubject to bacterial contamination forsome time or during some event eachyear. The overall issue is that the bacter-ial contaminants measured are indicatorsof fecal contamination, and, as such,indicators of the potential presence ofpathogenic microorganisms that cancause disease in humans that consumecontaminated shellfish or that areexposed through contact with water. Theconcentrations of the indicator bacteriaare generally quite low in many areasand most uses are supported. There hasbeen a clear decreasing trend in bacteri-al concentrations over the past ten yearsin most areas of coastal New Hampshire,largely as a result of upgrades in waste-water treatment facilities (WWTFs). How-ever, sources of contaminants persist for

all coastal waters, especially during andfollowing runoff events. This contamina-tion occurs at concentrations that com-monly require limiting uses of surfacewaters to protect humans frompathogens.

The issue of bacterial contamination ispresently being addressed by determin-ing sources of contaminants associatedwith stormwater runoff. Good documen-tation of the presence of elevated bacte-rial contaminants in stormwater runoffand their impact on water quality in sur-face waters exist. The actual sources ofthese bacteria are not known in all areas.Existing evidence suggests that runofffrom impervious areas, sewage cross-contamination in urban stormwater sys-tems, WWTFs, ineffective septic systemsand possibly waterfowl are the primesuspected sources for runoff-associatedcontamination.

A major problem caused by bacterialcontamination is the closure of shellfishbeds. Approximately 63% of estuarinewaters in New Hampshire are closed toshellfishing. Recreational shellfishing is apopular activity in the state, and the clo-sures represent not only limitations ofactivities that have long been treasuredbut also serve as the early warning sys-tem that other problems may also bepresent in the estuaries. Efforts to openshellfish-growing waters are recognizedto be simultaneously beneficial to otherliving resources and ecosystem func-tions, and continued efforts to openshellfish beds by improving water quali-ty should benefit the whole estuarineecosystem.

The public health significance of theelevated concentrations of bacterial indi-cators is not well understood. It has beendocumented in many studies in NewHampshire and throughout the worldthat the bacterial indicators used by stateagencies have significant limitations. Dif-ficulties in finding actual sources of bac-

EXECUTIVE SUMMARY

xvi

terial contamination may be related tosome of these implicit limitations of theindicators used to assess water quality.The implications and repercussions ofdetecting indicator bacteria should besupported with verification of the pres-ence or absence of actual pathogens. Apotential, emerging problem is the pres-ence of nonfecal-borne bacterialpathogens. These include Vibrio sp. andAeromonas sp. that have received recentattention by researchers at UNH. Natural-ly occurring bacterial pathogens cannotbe controlled by traditional eliminationof human pollution sources and thuspose a different, more insidious publichealth problem.

Trace metal and toxic organic contam-ination is also ubiquitous throughoutNew Hampshire’s coast. There is ampleinformation to provide an assessment ofthe spatial distribution and identificationof trouble spots relative to regional back-ground levels of these contaminants insediments and biota. Sites with elevatedconcentrations of contaminants includethe sediment depositional areas aroundthe Portsmouth Naval Shipyard onSeavey Island in particular, with otherhot spots for specific contaminants atvarious sites throughout the coast. Themost common contaminants present atelevated concentrations are chromium,lead, mercury, copper, zinc and PCBs.Contaminants like DDT (and metabo-lites) and PAHs are present at concentra-tions well above background levels, butnot at levels that are of concern tohumans and other biota, and are wellwithin expectations based on regionaldistributions of these compounds. Thelarge amount of information on tissueconcentrations of toxic compounds inshellfish serves as a useful database forassessing potential health risks forseafood consumption by humans. Themost acute documented concern is therelatively high concentrations of PCBs inlobster tissue and tomalley. There areconsumption advisories for tomalleyfrom lobsters in the Great Bay Estuaryand for bluefish throughout the coast.Concentrations of lead in mussels fromaround Seavey Island have been high

relative to published FDA “Action Lev-els”, while other metals have not exceed-ed these levels. On a regional scale,metals in mussels from sites in NewHampshire are elevated along with mus-sels from Massachusetts Bay and aresometimes the highest in the region. Met-als of concern include chromium, lead,mercury, cadmium, nickel and zinc.Organic contaminants in mussels havegenerally been well below action limits.However, mercury, PCB and DDT con-centrations in finfish and lobsters fromsites in the Great Bay Estuary and thenearby coast are of concern to bothhumans and wildlife. Other studies haveindicated a few instances of relativelyminor toxicity effects on marine andestuarine biota. Much of the toxic con-taminants present in New Hampshire’sestuaries is probably the result of historicsources, such as tanneries, landfills andpetroleum processing facilities. This his-torical contamination is largely stored inthe fine-grained sediments dispersedthroughout the estuaries. Identifiedsources that continue to load contami-nants to the estuaries include stormwaterrunoff from impervious surfaces, lowconcentration in some monitored pointsource discharges, pesticide applicationfor mosquito control and agriculturalpurposes, atmospheric deposition ofmercury and episodic oil spill events.Other suspected sources include munici-pal discharges, defense facilities andSuperfund sites, stormwater runoff andcontaminated groundwater. The less wellcharacterized sources warrant furtherinvestigation to determine if already ele-vated levels of some toxic contaminantsare increasing as a result of ongoingsources.

Nutrient loading occurs in all NewHampshire estuaries and their tributaries.Present and historical databases suggestthat nutrient concentrations within themain area of Great Bay have notchanged significantly over the past twen-ty years, and in fact, seasonal trendsappear to have been maintained in aconsistent fashion. No significant sys-temic eutrophication effects have beenobserved, with only isolated incidences

The State of New Hampshire has twoimportant estuaries along its approxi-

mately 220 miles of tidal shoreline. TheGreat Bay Estuary, the largest in NewHampshire, is a drowned river valley thatis similar to some of the estuaries foundalong the Maine coast. The Hampton/Seabrook Estuary is a bar-built estuarysituated behind barrier beaches and sur-rounded by expansive areas of salt-marsh. Though quite different in size,topography of the watershed, geomor-phology, hydrodynamics, and ecology,the Great Bay and Hampton Harbor estu-aries can have similar geographically-related problems. It is for this reason thatthese areas are collectively the main fociof the New Hampshire Estuaries Project.

Both estuaries have been studied byseveral organizations that include theUniversity of New Hampshire, JacksonEstuarine Laboratory (JEL), N.H. Fishand Game Department (NHF&G), NHDepartment of Environmental Services(NHDES), N.H. Office of State Planning(NHOSP), New Hampshire Departmentof Health and Human Services (NHD-HHS), Normandeau Associates, Inc. andthe U.S. Fish and Wildlife Service. Sub-stantial historic databases are availableon the physical and chemical propertiesof these estuaries, including sedimentol-ogy, hydrography and nutrient concen-trations. There are also extensive in-ventories of seaweed species, estuarinefish and invertebrates as well as standingcrop and distributional data for seagrass-es and marsh plants. There are numer-ous data layers for the area digitized onthe state Geographic Information System(GIS), including hydrography, landcover, land use, point sources of pollu-tion, potential nonpoint threats, bathym-etry, wetlands and intertidal macroalgae,and several others. Monitoring data aswell as other research efforts in GreatBay have been reviewed in a documententitled “The Ecology of the Great BayEstuary, New Hampshire and Maine: AnEstuarine Profile and Bibliography”(Short, 1992). This document summa-

rized the research and managementefforts in the Great Bay Estuary as of1991 and provides references fordetailed information. An extensive bodyof work on the Hampton Harbor Estuarywas compiled as part of the Environ-mental Impact Statement for the con-struction and operation of the Seabrooknuclear power plant. Monitoring effortscontinue today both in the estuary andoffshore at the cooling intake and outfallsites. The Hampton Harbor Sanitary Sur-vey (NHDHHS, 1994), a result of the1993 CORD Shellfish Taskforce’s efforts,describes water circulation, bacterialcontamination and the effect of stormsand tidal conditions in the estuary.

1.1.1 THE GREAT BAY ESTUARY

The Great Bay Estuary is a tidally domi-nated, complex embayment on thesouthern New Hampshire-Maine border(Figure 1.2). The estuarine tidal waterscover approximately 17 square miles(10,900 acres), with a 144-mile shorelineof steep wooded banks with rock out-croppings, cobble and shale beaches,and fringing saltmarsh. The estuaryextends inland from the mouth of thePiscataqua River between Kittery, Maine,and New Castle, New Hampshirethrough Little Bay to Great Bay proper, adistance of 25 km or 15 miles (Brownand Arellano 1979). The junction of LittleBay and the Piscataqua River occurs atDover Point. Little Bay turns sharply atCedar and Fox Points near the mouth ofthe Oyster River and ends at Furber Straitnear Adams Point. Great Bay beginsimmediately inland or “upstream” ofFurber Strait. With the exception of theeastern shore of the Piscataqua andSalmon Falls rivers which are borderedby southern York County, Maine, theestuary is entirely in Strafford and Rock-ingham Counties of New Hampshire.New Hampshire municipalities on theshores of the estuary include Ports-mouth, Newington, Dover, Rollinsford,Madbury, Durham, Newmarket, New-fields, Exeter, Stratham and Greenland.

4

1.1

GEOGRAPHICAL AND PHYSICAL SETTINGS

5

FIGURE 1.2

The Great Bay andHampton/Seabrook

Harbor estuaries and surrounding

municipality boundaries

Miles

Feet

Kilometers

1 .5 0 1

1000 7000

1 .5 0 1

The largest cities in the watershedinclude Rochester, Dover, Portsmouth,and Exeter and have estimated popula-tions of 28,726, 26,200, 22,830, and13,258, respectively (NHOSP, 1997). Dataon current and projected population andpopulation density for all towns in Straf-ford and Rockingham Counties are pre-sented in Appendix A.

Two-thirds of the 930 square mile Pis-cataqua River drainage basin is locatedwithin New Hampshire, with the remain-der in southern Maine (Reichard andCelikkol, 1978). Tidal waters from theAtlantic Ocean enter the estuarine systemat Portsmouth Harbor, flooding the threemajor portions of the Estuary; the Pis-cataqua River, Little Bay and Great Bay.The estuary derives its freshwater inflowfrom seven major rivers, four of whichare gauged by the U.S. Geological Survey(USGS) (the Lamprey, Oyster, Cocheco,and Salmon Falls rivers). The Lamprey,Squamscott and Winnicut rivers flowdirectly into Great Bay. The Salmon Falls,Cocheco, Bellamy, and Oyster riversflow into the estuary between FurberStrait and the open coast. River flowvaries seasonally, with the greatest vol-umes occurring as a result of springrunoff. However, the tidal component inthe estuary dominates over freshwaterinfluence throughout most of the year.

Freshwater input typically representsonly 2 percent or less of the tidal prismvolume (Reichard and Celikkol, 1978;Brown and Arellano, 1979), but the per-centage varies seasonally. Estimates offlow for all rivers (Appendix B) suggestthat the average combined freshwaterinflow is greater than 1000 cubic feet persecond. Approximately 50 percent of theaverage annual precipitation (42 inches)in the Great Bay Estuary drainage basinenters the estuary as stream flow(NHWSPCC, 1975).

Tidal height ranges from 2.7 m at themouth of the estuary to 2.0 m at DoverPoint, increasing slightly to 2.1 m at themouth of the Squamscott River. Thephase of the tide lags significantly mov-ing up the Great Bay Estuary from theocean and the slack tides can be as muchas 2.5 hours later in the Squamscott Riverthan at the mouth of the estuary. Strongtidal currents and mixing limit verticalstratification during most of the yearthroughout the estuary. Partial stratifica-tion may occur during periods of intensefreshwater runoff, particularly at theupper tidal reaches of rivers entering theestuary. The large tidal range duringspring tides results in exposure of exten-sive mudflats along the fringing areas ofthe Piscataqua River, Little Bay and thetributaries as well as large expanses of

6

Great Bay

S. M

IRIC

K

7

exposed tidal flats in the central part ofGreat Bay. High summer temperatures inthese shallow flats can reach 30°C in thesummer and -2°C during the coldest partof winter when much of Great Bay canfreeze over. Ice scour in winter and earlyspring can play a major role in both sed-iment transport and disturbances to sub-merged aquatic vegetation and benthicfauna.

The observed flushing time for waterentering the head of the estuary is 36tidal cycles (18 days) during high riverflow (Brown and Arellano, 1979). Tidescause considerable fluctuations of waterclarity, temperature, salinity and currentspeeds, and have a major impact on bot-tom substrata. Shallow areas of the estu-ary are also greatly affected bywind-wave conditions which can influ-ence grain size distributions and sedi-ment transport throughout the estuary.Waves resuspend sediments, increasingturbidity levels well above levels attrib-uted to tidal currents alone (Anderson,1972). A horizontal gradient of decreas-ing salinity exists from the mouth of theharbor to the tidal reaches of the tribu-taries and the upper portions of GreatBay. The range of this gradient (0-30 ppt)depends on tidal cycle, season and rain-fall conditions.

The Great Bay Estuary has a variety ofdifferent habitats including approximate-ly 1,000 acres of saltmarsh, 52 acres ofmajor oyster beds, 2,575 acres of scat-tered clam flats, 5,000 acres of subtidaleelgrass, extensive intertidal and subtidalmacroalgal cover, mudflats and rockyoutcroppings and islands. The subtidalsubstrate in the lower estuary is primari-ly rock and cobble, with sand and mud-sand mixture in the intertidal andnearshore subtidal areas. Some hard sub-strate can be found in channel areas ofthe upper estuary and tidal rivers, but thedominant substrata are sandy mud andsilt. Because of this habitat diversity,Great Bay Estuary supports a wide vari-ety of flora and fauna described in moredetail in Chapter 3: Living Resources.

Land cover for the watershed of theGreat Bay Estuary, mapped using 1988

and 1990 LANDSAT Thematic Mapperimagery, has been digitized on the stateGIS system. Land cover shows the water-shed is primarily forested, with smallerpercentages of other land cover cate-gories Table 1.1, Appendix C). Most ofthe urban land is concentrated in themunicipalities of Rochester, Dover,Portsmouth, and Exeter.

Land use information for the water-shed, developed in the 1980s and early1990s by Rockingham and StraffordRegional Planning Commissions, has alsobeen mapped and digitized on the stateGIS system (Appendix C). Land use sur-rounding the Great Bay Estuary rangesfrom urban/industrial near the mouth ofthe Piscataqua River and in the cities andtowns located at the head of tide of eachof the tributaries, to rural, residential andundeveloped private and public lands.The Portsmouth Naval Shipyard, a majormilitary base, is located on Seavey Islandin Portsmouth Harbor, and the formerPease Air Force Base in Newington andPortsmouth is currently under commer-cial development as the Pease Interna-tional Tradeport. A portion of the estuaryis part of the National Oceanic andAtmospheric Administration’s (NOAA)National Estuarine Research Reserve Pro-gram and is managed by NH Fish andGame Department. Just over 1,000 acresof the former Pease Air Force Base arenow the Great Bay National WildlifeRefuge, managed by the U.S. Fish andWildlife Service. Land and shorelineownership around the Great Bay Estuaryand throughout its tidal waters is pre-dominantly private, with some lands pro-tected or in government ownership(Short and Webster, 1992). For landswithin 300 feet of the tidal waters of theGreat Bay Estuary system, 38% is devel-oped, 18% is permanently protected, 7%is undevelopable and 37% is developable(Rubin and Merriam, 1998). Acquisitionof lands for conservation easements is anongoing process, with both government(U.S. Fish and Wildlife Service, N.H. Fishand Game Department, Great BayNational Estuarine Research Reserve)and private programs operating.

1.1.2 HAMPTON/SEABROOK ESTUARY

The Hampton/Seabrook Estuary is a tidal-ly dominated, shallow, bar-built estuarylocated at the extreme southeast cornerof New Hampshire (Figure 1.2). It islocated entirely in Rockingham Countyand is bordered by the towns of Hamp-ton, Hampton Falls and Seabrook. TheEstuary is roughly rectangular in shape,has approximately 72 miles of tidalshoreline and has a total area at high tideof approximately 475 acres. The topogra-phy of the 47 square mile watershed isrelatively flat with approximately 17 per-cent (5,000 acres) of saltmarsh. Eightypercent of the watershed is in NewHampshire, with the remainder in Mass-achusetts. There is one harbor entrancethrough which all tidal waters enter andexit. Tides are semi-diurnal with a meantidal range of 2.5 meters and spring tidalrange of 2.9 meters. During averagewind conditions approximately 88 per-cent of the water in the estuary isexchanged on each tide (PSNH, 1973).The typical substratum is more coarse-grained than that found in the Great BayEstuary, and more typical of a barrier sys-tem. The estuary receives freshwaterinput from the Taylor River and Hamp-ton Falls River (which converge to formthe completely tidal Hampton River) tothe north; the Browns River and MillCreek to the west; and the Blackwater

River to the south. Numerous small tidalcreeks from the surrounding wetlandsalso drain into the estuary. River flowsvary seasonally with the highest flowsoccurring in spring due to snowmelt andprecipitation. Average annual precipita-tion is approximately 42 inches. Totalmean freshwater discharge has been esti-mated to be 4.08 cubic ft/sec (NHDHHS,1994a) and is minimal when comparedto the average tidal flow of 22,000 cubicft/sec. Water depth is relatively shallow,ranging at mean low tide from less thanone meter in the tidal creeks and riversto over six meters at the harbor entrance.Most of the harbor channels have a lowtide depth of one to three meters.

During periods of light winds, thetidal flows dominate water circulation.Circulation can change considerably,however, in response to high wind andstorms. Strong westerly and northwester-ly winds alter tidal flows by forcing sur-face waters out of the mouth of theestuary, while during northeast storms,surface waters are pushed landward,impeding the seaward flow of ebb tidewater (NAI, 1977). The estuary is gener-ally well mixed with little vertical stratifi-cation, though some stratification doesoccur, particularly in the tidal rivers andcreeks during high flow periods (NHD-HHS, 1994a).

Perhaps the most striking feature ofthe Hampton/Seabrook Estuary is the

8

The Hampton/Seabrook Estuary

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9

large expanse (5,000 acres) of contigu-ous salt marsh that surrounds the estuary.The estuary is also the most popularlocation in coastal New Hampshire forrecreational harvesting of softshell clams.Mussels, lobsters, and a variety of finfishare also present. Sandy beaches bothwithin and adjacent to the estuary are amajor tourist attraction. Some of the lastremaining sand dunes in coastal NewHampshire are located in the area. TheSeabrook dunes, damaged by a series ofcoastal storms, were recently restoredwith sand and American beach grass.

Land cover for the Hampton/Seabrook Estuary Watershed, mappedusing 1988 and 1990 LANDSAT ThematicMapper imagery, has been digitized onthe state GIS system (Table 1.1). Landcover shows the watershed is primarilyforested, but not to the extent (on a per-centage basis) of the Great Bay EstuaryWatershed. A large amount of urban landis concentrated near the estuary in theTown of Hampton (estimated 1996 pop-ulation of 13,003).

Land use information for the water-shed, developed in the 1980s and early1990s by Rockingham Planning Commis-sions, has also been digitized on the stateGIS system (Appendix C). The HamptonHarbor area is the major summer resortarea along the New Hampshire coast.Development bordering the estuary isprimarily residential and concentrated inthe beach areas on the eastern shore. Ofthe lands within 300 feet of the tidalwaters of the Hampton/Seabrook Estu-ary, 14% ar edeveloped, 10% are perma-nentlyt protected, 4% are developableand 71% are deemed undevelopable, pri-

marily because of the large expanse ofsalt marsh around the estuary.

Commercial development consistsmostly of shops, hotels, and restaurantsthat support the tourist industry. Thepopulations of both Hampton andSeabrook double in the summer toapproximately 23,000. Total daily beachpopulation, which includes daily visitors,vacationers at the hotels and motels(~30,000) and permanent and summerresidents, can be as high as 100,000.Industrial activity in the watershedincludes plastics, shoe and furnituremanufacturing and metal fabrication.Most of these industries are small withthe largest employing 1,000 people andtotal industrial employment at approxi-mately 3,000. Seabrook nuclear powerstation, located on the western shore ofthe estuary, is a prominent feature.

1.1.3 BEACH AND DUNE SYSTEMS

The New Hampshire coast between theGreat Bay and Hampton/Seabrook estu-aries has significant areas of beaches anddunes. The beaches are heavily used inthe summertime for bathing and surfing,and have experienced severe erosionduring several recent storm events. Thebeaches and the rocky intertidal areashave been maintained to protect privateand public properties and to provideconditions at the beaches that allow theeconomically-important tourist trade toremain viable. The historical extent ofthe dune areas has been drasticallyreduced by human development. Someof the remaining dunes, including thosein Seabrook, have undergone somerestoration.

GREAT BAY ESTUARY HAMPTON/SEABROOK ESTUARYCATEGORY Acres % of Total Acres % of Total

Forested 296,070 66 10,094 40Wetland 44,703 10 5,392 21Urban 43,944 10 5,800 23Agriculture 28,418 6 2,039 8Disturbed 8,494 2 380 2Cleared 9,240 2 400 2Water 17,211 4 1,030 4

Watershed land cover for the New Hampshire portions of the Great Bay and Hampton/Seabrook Harbor estuaries.

TABLE 1.1

1.2

BIOLOGICAL SETTING New Hampshire’s estuaries are com-

posed of a variety of habitats. Theyserve as nursery areas for commerciallyimportant fish and shellfish species andsustain runs of numerous anadromousspecies. The primary producers include adiverse community from benthic diatomsto salt marshes and from microscopicphytoplankton to seaweeds and eelgrass.Along with the estuarine aquatic habitats,the surrounding terrestrial and wetlandsareas support a variety of birds andmammals.

1.2.1 FISH AND SHELLFISH

Because of the diversity of habitats, NewHampshire’s estuaries support an impres-sive array of living resources. The estuar-ies sustain runs of anadromous sturgeon,shad, alewives, lampreys, smelt andsalmon that spawn in the freshwater por-tions of the rivers and streams. Freshwa-ter areas of the rivers and streams inHampton Harbor are directly accessibleby anadromous fish, and in all the majorrivers in the Great Bays Estuary, whichwere dammed in the 1800s forhydropower, fish ladders have been built

and maintained to allow anadromousspecies access to freshwater spawningareas. The estuaries also serve as nurseryareas for commercially important speciessuch as lobsters, winter flounders, cod,pollack, eels and hake. Both juvenile andadult striped bass can be found inincreasing numbers between May andOctober as they forage on the abun-dance of baitfish such as silversides andsmelt. The remarkable recovery of theeast coast stocks of striped bass has beenin part due to the availability of summerfeeding areas such as Great Bay andHampton Harbor. Berrys Brook in Rye, atributary to the lower Piscataqua River,has a rare population of sea run browntrout. Shellfish are also abundant. Thereare 52 acres of oyster beds, over 2500acres of scattered clam flats and signifi-cant areas with blue mussel beds, razorclams and scallops in Great Bay Estuaryand its tributaries (Appendix D). Hamp-ton Harbor supports abundant popula-tions of softshell clams (approximately2000 bushels) and blue mussels. Aninventory of invertebrates and fishspecies is listed in Appendix E.

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1.2.2 BIRDS AND MAMMALS

A diverse bird population occurs withinthe estuaries of coastal New Hampshire,with as many as 110 species (excludingupland birds) observed using the estuar-ies. Coastal New Hampshire is part of theAtlantic flyway and is an importantmigratory stopover as well as winteringarea for waterfowl. Seabirds, wadingbirds, shore birds, estuarine birds ofprey, waterfowl and diving birds arefound throughout the estuarine areas.

Seabirds (i.e. cormorants and gulls)are year-round residents of Great Bay.Herring gulls and great black-backedgulls are common within the estuary.The common tern (threatened in N.H.)nests in several areas of Great Bay andHampton Harbor. Double-crested cor-morants are present from April toNovember. Waterfowl, including blackducks and Canada geese, occur in falland winter. Goldeneyes, scoters, scaups,buffleheads, mergansers and grebes arealso seasonal visitors in Great Bay Estu-ary. A year-round population of muteswans, now totaling more than 60 birds,nests along the shores of Great BayEstuary and spends the winter in theopen waters of the bay. The great blueheron is the most prominent wadingbird, occurring primarily from April to

October. Other wading species includesnowy egrets, green herons, black-crowned night herons, glossy ibis,greater and lesser yellowlegs, and leastsandpipers. Upland sandpipers are arare species, though there is a nestingpopulation adjacent to the runway atthe Pease International Tradeport. Com-mon terrestrial species include theAmerican crow, belted kingfisher, ruffedgrouse, and wild turkey.

Several endangered and threatenedbird species, including bald eagles,common terns, upland sand pipers,marsh hawks, ospreys and commonloons utilize part of Great Bay Estuary’sdiverse habitat at various times of theyear. The estuary supports the largestwinter population of bald eagles in NewHampshire. During recent winters up tofifteen eagles have occupied this win-tering area simultaneously during earlyDecember through March. Ospreys,common loons and pied-billed grebesforage in the bay during migration; oneosprey pair nested on the Bay in 1990,and more have nested since.

Mammals common to the Great Bayand Hampton/Seabrook estuaries includeotters, minks, and beaver. Muskrats nestand overwinter in many areas of the baysand rivers, and harbor seals are frequent-ly observed in fall, winter and spring.

Snowy Egret

S. M

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1.2.3 PRIMARY PRODUCERS

Primary producers in the Great Bay andHampton/Seabrook estuaries includephytoplankton, benthic diatoms, salt-marsh plants, brown, red and greenmacroalgal species and eelgrass. Phyto-plankton support a broad spectrum ofplanktonic consumers including bivalve,crustacean and fish larvae, as well as thelarge populations of sessile filter feedinginvertebrates. Grazers such as snails,deposit feeding worms and other inver-tebrates feed on the benthic diatoms thatgrow on the exposed tidal flats.

Approximately 5,000 acres of eelgrass(Zostera marina) occurs in the Great BayEstuary, though none occurs in HamptonHarbor. Eelgrass supplies the estuarinefood web with organic matter, helps tostabilize sediment, and provides habitatfor juvenile fish and invertebrates. Fol-lowing substantial loss of eelgrass coverin the 1980s to an eelgrass wasting dis-ease, eelgrass beds have expanded in thepast several years and the populationsappear to be in good condition. Theimportance of eelgrass beds is reflectedin state and federal wetland regulatoryactions that may require substantial miti-gation, as was the case for the expansionof the Port of Portsmouth in 1993.

A total of 219 seaweed species areknown from New Hampshire, includingthe Isles of Shoals (Mathieson and Hehre1986, Mathieson and Penniman 1991). Ofthis total, 169 taxa (77.2% of total) arerecorded from the Great Bay Estuary,including 45 Chlorophyceae, 46 Phaeo-phyceae and 78 Rhodophyceae. A vari-

ety of seaweed species occur withinGreat Bay that are absent on the openAtlantic coast north of Cape Cod. Thesespecies, which have a disjunct distribu-tional pattern, may represent relict popu-lations that were more widely distributedduring a previous time when coastalwater temperatures were warmer (Bous-field and Thomas 1975). Alternatively,they may have been introduced from thesouth. These seaweeds (e.g. Gracilariatikvahiae, Bryopsis plumosa, Dasya bail-louviana, Chondria tenuissima, Lomen-taria clavellosa, Lomentaria orcadensisand Polysiphonia subtilissima) grow andreproduce during the warm summer andare able to tolerate colder winter temper-atures (Fralick and Mathieson 1975,Mathieson and Hehre 1986). Several ofthese seaweed taxa and several inverte-brates exhibiting this same pattern alsooccur in the Great Salt Bay at the head ofthe Damariscotta River in Maine, an areasomewhat similar to Great Bay. The dis-junct distributional pattern described forthe seaweeds is also found for severalmarine/estuarine invertebrates (Bousfieldand Thomas 1975, Turgeon 1976).

There are approximately 1,000 acresof saltmarsh in the Great Bay Estuary andover 5,000 acres of saltmarsh in theHampton Harbor Estuary. Though thesemarshes are dominated by Spartinaalterniflora and Spartina patens, a totalof 69 species of plants have been identi-fied in New Hampshire saltmarshes(Short and Mathieson, 1992). In additionto the rare and endangered birds previ-ously mentioned, a number of rare andendangered plants are also found withinthe Great Bay Estuary. These speciesinclude the prolific knotweed (Polygon-um prolificum), Eastern lilaeopsis(Lilaeopsis chinensis), Turks-cap lily (Lil-ium superbum), marsh elder (Ivafrutescens), stout bulrush (Scirpus robus-tus), exserted knotweed (Polygonumexsertum), and the large saltmarsh aster(Aster tenufolius). New Hampshire’s salt-marshes have received a great deal ofattention from resource managers overthe past decade concerned aboutenhancing the functions of these impor-tant natural communities.

12

Eelgrass

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1.3

HUMAN SETTING

13

The Great Bay and Hampton/Seabrook estuaries are extremely

important to the local, regional, state,and national economies. From the timeof first European settlement, the GreatBay Estuary was a center of commercefor natural resource based industriessuch as commercial fishing and logging.Virgin forests, bountiful runs of anadro-mous fish such as salmon, shad, stur-geon and river herring, as well asplentiful shellfish resources were thebasis of a rapidly expanding economy.Plentiful timber and tidal water access tothe towns gave rise to a large shipbuild-ing industry during the 1700s. Sailingbarges called gundalows carried rawmaterials and manufactured goods tothe towns in the estuary. During the19th century, shoe and textile manufac-turing became important and mills werebuilt in all towns with access to naviga-ble waterways. Increasing populations,lack of sewage treatment, pollutionfrom sawmills and other industries, aswell as unwise exploitation of naturalresources, led to habitat degradationand declines in important fish and shell-fish species. Abatement of pollutionsources began in the 1940s and contin-ues today, and the water quality andhabitat areas have made a significantrecovery.

Today there are varied commercialactivities centered on the estuarine sys-tems. Energy production facilities arelocated on the lower Piscataqua River aswell as on the shore of Hampton Harbor.Shipping of lumber, mineral salt, gypsum,scrap metal, and other products occursfrom the Port of New Hampshire inPortsmouth. The estuarine systems act asnursery areas for several species of fishthat support local and regional fisheries inthe Gulf of Maine. Although commercialfishing and shipping are important to theGulf of Maine regional economy, tourismand recreation have become an increas-ingly important part of the New Hamp-shire Seacoast economy. The recreationalindustries supported by the activitiesdescribed below are dependent on goodwater quality and a healthy ecosystem.

1.3.1 RECREATIONAL RESOURCESAND VALUES

Recreational activities in the Great Bayand Hampton/Seabrook estuaries areextensive and diverse, and have becomea significant portion of the New Hamp-shire Seacoast economy. Boating, fishing,swimming, SCUBA diving, and otherwater sports are important recreationalactivities. Passive forms of recreationsuch as birdwatching and sight-seeingare also common.

E. F

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1.3.1.1 Boating

Boating activities in the estuarine systemsinclude sailing, fishing, water skiing,wind surfing, rowing, kayaking andcanoeing. Boater registration recordsfrom 1993 indicate a total of almost 3,500boats registered for tidal waters (notethat the registration category is “freshand tidal water” thus, not all of theseboats are in the tidal waters all year). Justover 3,100 (90%) of these boats were inthe “private/rental” class, while theremaining 10% were in the “charter/com-mercial” class (N.H. Dept. of Safety,1994). During the 1980s, the Great BayEstuary experienced a dramatic increasein boating activity as evidenced by thenumber of mooring permits issued bythe state. The rate of increase leveled offfollowing the adoption of the HarborManagement Plan.

Most of the approximately 1,400moorings in N.H. tidal waters are usedby pleasure boaters, with the rest of themooring permits going to commercialboats and to commercial lease holders(marinas). The high demand for moor-ings is reflected in the length of themooring waiting list, maintained by theN.H. Port Authority. There are currentlyalmost 550 people waiting for a moor-ing, with the length of the wait rangingfrom three to 20 years, depending onthe location requested (N.H. PortAuthority, 1995).

1.3.1.2 Shellfishing

Shellfishing is also an important recre-ational activity in the estuaries. The GreatBay Estuary supports a large recreationalshellfishery for oysters, clams and mus-sels. Oysters are the predominant shell-fish resource utilized in Great Bay,although Little Harbor supports moreconcentrated populations of clams. Majoroyster beds are located in Great Bayproper, as well as in the Piscataqua, Bel-lamy, and Oyster rivers, with scatteredpockets of oysters also found throughoutthe estuary (Figure 1.3). The estimateddollar value of oysters in major beds wasnearly $1.6 million in 1981 and $3 millionin 1994. Approximately 5,000 bushels of

oysters, valued at $300,000 are harvestedannually by the 1,000 license holders(Manalo et al., 1991). Recreational har-vesting of shellfish in the Great Bay Estu-ary is currently limited to most of GreatBay and Little Bay, with the upper Pis-cataqua River, and the smaller tidal riversclosed to harvesting due to bacterial pol-lution (Figure 1.4). The harvesting ofsoftshell and razor clams in Great Bay,though difficult, has become intensifiedbecause of the closure of more popularclamming areas such as the flats inHampton and Little Harbors.

The principal shellfish resource inHampton Harbor is the soft shell clam,located in five major resource areas (Fig-ure 1.5). These flats had been closedsince 1988, but with the conditionalreopening of some of the flats in the fallof 1994 and further openings in 1995 and1998 (Figure 1.6), almost 3,000 clamminglicenses were sold in 1994 (up from 239licenses in 1993). Prior to clam bed clo-sures in 1988, the average number oflicenses sold in the State between 1971-1987 was 6,400. The clam flats and mus-sel beds in Rye, Little and Portsmouthharbors, the lower Piscataqua River, theBack Channel and, in 1998, the opencoast (Figure 1.7), remain completelyclosed to recreational harvesting(Figure1.8). The contribution of recreationalshellfishing to the local and state econo-my has been estimated to be $3 millionper year (Manalo et al., 1992).

1.3.1.3 Fishing

The Great Bay Estuary supports a diversecommunity of resident, migrant, andanadromous fishes, many of which arepursued by recreational fishermen. Themost abundant species include Atlanticsilverside, rainbow smelt, killifish, riverherring, Atlantic tomcod, white perch,winter and smooth flounders. Year-roundresidents such as Atlantic silverside, killi-fish, Atlantic tomcod, winter flounder(juveniles), and smooth flounder arefound throughout the estuary. Recre-ational fishermen pursue striped bass,bluefish, salmon, eels, tomcod, shad,smelt, and flounder. Fishing is not limitedto boat access, as cast or bait fishing is

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15

Oyster BedsScattered OystersSoft-shell Clams

Great BayShellfish Beds

FIGURE 1.3

Shellfish resources inGreat Bay, Little Bay,

and tributaries.

Great BayFIGURE 1.4

1998 Shellfish waters classification for the

Great Bay Estuary. Open

Closed

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FIGURE 1.5

Hampton/Seabrook Harbor clam flats

FIGURE 1.6

1998 Shellfish waterclassification for Hampton/SeabrookEstuary

1

4

3

2

5

1 Common Island2 Hampton/Browns River Confluence3 Browns River Area4 Middle Ground5 The Willows

Open

Closed

17

FIGURE 1.7

Shellfish resources inPortsmouth, Rye, and

Little Harbors.

FIGURE 1.8

Shellfish classification for Portsmouth, Rye,

and Little Harbors and the northern

open coast.

Unclassified (closed)

Soft-shelled Clams

done from the shore in many places andfrom the bridges crossing the estuary.Several charter boat companies in theGreat Bay Estuary take fishermen to pur-sue striped bass, bluefish, and pollack,while companies operating out of Hamp-ton Harbor carry fishing parties to the off-shore waters to pursue cod, bluefish,flounder, mackerel, and other fish. Oneof the major winter activities in Great andLittle Bays is ice fishing for smelt. Thesmelt fishery in Great Bay occurs primari-ly in the Greenland Cove, Lamprey River,Squamscott River and Oyster River areasfrom early January to March. The N.H.Fish and Game Department has pursuedstocking and monitoring efforts on select-ed fish stocks (e.g., shad and Atlanticsalmon) in order to enhance recreationalfisheries (NHF&G 1989). Another impor-tant recreational fishing activity is thetrapping of lobsters. Almost 150 recre-ational lobstermen set traps throughoutthe Great Bay and Hampton/Seabrookestuaries, with the Portsmouth Harborarea being a popular location.

Studies by N.H. Fish and Game con-sultants identified substantial sums ofmonies spent on marine recreationalfishing. An estimated 88,000 saltwateranglers spent over $52 million in 1990 onfishing-related activities (approximately$600 per person). The largest expendi-tures were for food and beverages, auto-mobile fuel, charter/ party boat fees, baitand fishing tackle, and boat fuel. A sub-stantial amount of that total is estimatedto come from expenditures in Great Bayestuarine activities.

1.3.1.4 Passive Recreation

There are several types of passive recre-ation that are common in and around theGreat Bay and Hampton/Seabrook estu-aries. One of the major attractions ofNew Hampshire’s estuaries, particularlyGreat Bay, is the beautiful scenery. Sev-eral large tour boats bring groups intothe Bay to see the fall foliage and toenjoy the water views and largelyunspoiled shorelines. Fishermen, sports-men, and boating enthusiasts frequentthe estuary year-round. Though the sce-nic use of Great Bay is enjoyed primari-

ly by way of boating, a number of pub-lic access areas, parks, and nature trailsprovide sweeping views of the Great BayEstuary. These areas include:

■ Adams Point in Durham

■ Cedar Point in Durham

■ Hilton Park in Dover

■ GBNERR Sandy Point Discovery Center in Stratham

■ Chapman’s Landing in Stratham

■ Prescott Park in Portsmouth

■ Bellamy and General Sullivan Bridges in Dover

■ Bellamy River Wildlife ManagementArea in Dover

Numerous state parks exist along theAtlantic coastline from Rye to Hampton,providing swimmers, sunbathers, fisher-men, and picnickers with both sandybeaches and rocky shorelines. Severaltowns around the estuary maintainaccess and recreation facilities, includingWagon Hill Farm in Durham (OysterRiver), Fox Point in Newington (LittleBay), Pierce Island and Prescott Parks inPortsmouth (Piscataqua River), as well asaccess points in Dover (Cocheco River),Newmarket (Lamprey River), and Exeter(Squamscott River). Historic sites such asFort Constitution in New Castle, Straw-berry Banke in Portsmouth, and FortMcClary and Fort Foster in Maine arealso located on the Piscataqua River.

Bird watching by an active seacoastchapter of the Audubon Society, as wellas by other groups, is increasing in pop-ularity. A volunteer group now conductsregular surveys of waterfowl, seabirds,songbirds, and raptors for the Great BayNational Estuarine Research Reserve.Great Bay is a favored wintering site forbald eagles, with as many as 15 individ-ual birds having been observed over thecourse of a winter. Nesting ospreys arealso a popular attraction. The opening ofthe Great Bay National Wildlife Refuge inthe fall of 1995 has resulted in increaseduse of the area for bird watching andenjoyment of nature.

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1.3.2 COMMERCIAL RESOURCES AND VALUES

1.3.2.1 Industry and Shipping

Commercial uses of the Great Bay Estu-ary are primarily concentrated inPortsmouth Harbor and along the NewHampshire side of the Piscataqua River.The Port of New Hampshire inPortsmouth Harbor, a center of deep-water cargo shipping activities includingfuel oils, wire cable, cement, scrap metal,salt, gypsum, coal, propane, gasoline,and other products, supports numerousindustries located along the lower Pis-cataqua River. Tonnage for 1992 was justover 4,100,000 tons, with just over half ofthe total being oil shipments. Additional-ly, the Portsmouth Naval Shipyard, locat-ed on Seavey Island in PortsmouthHarbor, uses the estuary to provide sub-marine access to repair facilities and forshipping activities.

1.3.2.2 Fishing

Commercial fishing in New Hampshireoccurs mainly offshore, and is based infishing cooperatives in Portsmouth andSeabrook. However, eels, lampreys andbaitfish such as silversides, mummichogsand river herring are harvested commer-cially in the Great Bay Estuary. A sub-stantial commercial lobster fishery existsin the Great Bay Estuary and othercoastal waters, with almost 300 lobster-men harvesting nearly 881,300 pounds,valued at approximately $5-6 millioneach year. Studies conducted for the Fishand Game Department estimate over$1.8 million is expended annually bycommercial fishing interests.

Several small charter boats take pas-sengers fishing for striped bass, blue-fish, and pollack in the Great and Littlebays, while charter boats based inHampton and Seabrook take passengersoffshore to pursue cod, flounder, mack-erel, and others.

Four commercial shellfish aquacultureoperators in the Great Bay Estuary wereactive in the 1970s and 1980s. The only

shellfish aquaculture business operatingtoday is located in Spinney Creek on theMaine side of the Piscataqua River. How-ever, there has been recent interest inreviving aquaculture in New Hampshire.

1.3.2.3 Tourism and Recreational Industries

Tourism has become a major industry inthe New Hampshire Seacoast, and theSeacoast Region is an important area forthis industry in the state. Approximately10 percent of all visitors to New Hamp-shire come to the Seacoast, exceededonly by the White Mountains and LakesRegions (Institute for New HampshireStudies, 1993). The Travel and Tourismindustry, which includes businesses suchas hotels/motels, marinas and relatedboating stores, tour boats, retails stores,fishing charter boats, parks and otherrecreational facilities, and restaurants,supports just over 15 percent of the jobsin the Seacoast, making it the region’ssecond largest industry (Table 1.2). Ahealthy estuarine system is critical tomaintaining this portion of the seacoasteconomy. In a survey of summer vaca-tioners in 1993, respondents were askedwhat their “image” of New Hampshirewas. The most common responses were“scenic,” “clean,” and “beautiful” (Insti-tute for New Hampshire Studies, 1993).Closed shellfish beds and other visiblesigns of pollution, therefore, clearlydetract from the estuaries’ value to thetourism industry.

Industry Total Employment (%)

Manufacturing 32.2Travel and Tourism 15.3Other Services 15.2Other Retail 12.1Government 7.7Transportation/Public Utilities 7.5Agriculture/Mining/Construction 7.1Financial/insurance/Real Estate 2.9

Employment in the New Hampshire seacoast economy. Data from Institute for New Hampshire Studies (1993).

TABLE 1.2

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he ability of an estuary to sup-port a variety of unique habitats,diverse assemblages of organ-

isms and a variety of human activities islargely dependent on environmentalquality. Waters that can affect estuarinewater quality include groundwater, pre-cipitation, wetlands and surface waters,including estuaries, rivers, lakes, streamsand ocean waters. Water quality in turn isdependent on the types and amounts ofcontaminants that enter estuaries as aresult of human activities, and the naturalprocesses of an estuary that transform,assimilate and transport contaminants.Both humans and natural ecosystemsdepend on certain levels of water qualityfor providing safe drinking water and ashabitat for sustained food sources. Thereare many other human uses of the estu-ary and its surrounding environment,some of which may contribute to con-taminant loading. The following chapteris organized by contaminant category inorder to summarize information for eachcategory, to frame issues, to assess thesignificance of issues and to develop thecontext to formulate corrective manage-ment strategies where necessary. Gener-ally speaking, the primary contaminantsof concern for most estuaries, includingthose in New Hampshire, are:

1 microorganisms from improperlytreated sewage, urban stormwaterrunoff and other nonpoint sources;

2 nutrients from point sources (sewagetreatment plants) and nonpointsources (riverine input, surface runoff,septic systems, atmospheric deposi-tion, etc.);

3 toxic contaminants (trace metals,organics, oil, pesticides, etc.) whosesources may be historic (chromium,pesticides), potential (oil) or current(metals and PAH’s from stormwater,industrial and municipal wastewaterand atmospheric deposition);

4 sediments of upland watershed orriparian origin that are carried into theestuaries by runoff.

These contaminants are listed in noparticular order of priority. This sectionof the report describes the current statusand spatial and temporal trends of thesecontaminants in coastal New Hamp-shire, and provide information on docu-mented and suspected sources.Documented and potential impacts toliving resources are also discussed. Theterm ‘contaminant” is used most oftenbecause the alternative term, ‘pollutant’,is only used when there are biologicaleffects associated with the presence ofchemicals in the environment.

2 PRESENT STATUS AND HISTORICAL TRENDS IN WATER QUALITY

T

Overflow pipe on North Mill Pond

2.1.1 BACKGROUND

The Federal Water Pollution Control Act,as reauthorized by the Water Quality Actof 1987, requires New Hampshire to sub-mit a report that describes the status ofground and surface waters to the US Envi-ronmental Protection Agency (USEPA)and Congress every two years. These“305(b)” reports have been publishedevery two years since 1988. Surfacewaters are assessed according to overallquality and use support, individual useimpairments, causes of impairments,trends in water quality, wetlands andpublic health/aquatic life concerns. Moredetailed summaries of overall quality/usesupport and some individual use impair-ments are summarized in Appendix F forthe 1988 through 1996 305(b) reports.

Overall water quality and use supportdata are separated into freshwater andtidal waters, then by defined areas in thecoastal area. The classification for usesupport provides information on the milesof freshwater streams and rivers in theCoastal and Piscataqua River basins sup-

porting all uses. The tidal waters includethe open ocean (Isles of Shoals), coastalshoreline and the estuaries as separateareas. Figures 2.1 and 2.2 summarize thetrends in water quality for these watersfrom 1992 to 1996. Water bodies are clas-sified as either “fully supporting”, “partial-ly supporting” or “not supporting” alluses. The definitions for these classifica-tion categories are as follows:

■ fully supporting: criteria for con-taminants or conditions are notexceeded, or are exceeded infre-quently for any measurement, andno bans/advisories are in effect;

■ partially supporting: criteria for contaminant exceeded at low tomedium frequency for any meas-urements, restricted consumptionadvisory or ban in effect, or adviso-ry lasting only a short period;

■ not supporting: criteria exceeded at medium frequency, advisory periods too long or too frequent, or “no consumption” ban in effect.

22

2.1

OVERALL WATER QUALITY AND USE SUPPORT

1992 1994 1996

Coastal Basin

Piscataqua River Basin

80%

95% 97% 96%100% 99%

FIGURE 2.1 Percent of classified coastal waters as fully supporting all uses: Freshwater (NHDES, 1996b).

23

These classification categories aredefined in more detail for the differentindividual use categories, includingaquatic life use, drinking water use,recreational use and fish consumptionuse, based on USEPA guidelines. Theaquatic life use category criteria arebased on conditions where chlorine,ammonia or other toxicants cause viola-tions based on acute toxicity tests, orconditions relative to dissolved oxygen,pH or temperature exceed criteria limits.

The overall program of assessingwater quality and use support hasevolved since 1988. In general, less infor-mation was available in earlier years forassessing surface waters, and the assess-ment of some uses was incomplete. Morerecent data, showing a high degree ofsupport for all uses, are more completeand therefore more accurate relative to agreater range of contaminants. Betweenthe 1990 and the 1992 305(b) reports, theUSEPA suggested that New Hampshireand other states use a new database(Waterbody System software; River ReachFile-RF3) for defining hydrologic features.The miles for surface waters reported byNew Hampshire decreased from 14,544

to 10,841 miles as a result of differencesin scale used to trace hydrologic features.In previous years, NHDES only assessed,or made use support decisions, on 1348miles statewide. The assessed waterstended to be “problem” waters. In 1992and thereafter, NHDES has used anyavailable information to assess all waters,and area/mileage assessed for all fresh-water and estuarine waters thus increasedfrom 1990 to 1992. Other changes in theprogram resulted from passage of HB560, amending RSA 485:A, by the legisla-ture in 1991. Thereafter, all existing ClassC waters were reclassified and upgradedto Class B, with the goal of attaining“fishable and swimmable” conditions inall surface waters. HB 560 also includedadoption of different bacterial indicatorsfor freshwater and tidal waters. Based onEPA recommendations, fecal indicatorswere changed as Escherichia coli wasadopted for freshwater and enterococciwas adopted for tidal recreational waters.RSA 485:A was also changed to allow foruse of any indicator adopted by theNational Shellfish Sanitation Program(NSSP) for classification of shellfish grow-ing waters.

Percent of classified coastal waters as fully supporting all uses: Tidal water (NHDES, 1996b). FIGURE 2.2

2.1.2 STATUS AND TRENDS OF OVERALL WATER QUALITY AND USE SUPPORT

There has been a general improvementin water quality in the fresh and tidal sur-face waters of New Hampshire since1988 that can be attributed in large partto improvements in sewage treatmentfacilities. In the Coastal Basin, at least75% of the rivers and streams have fullysupported all uses since 1988, improvingto 100% support of all uses in 1996 (Fig-ure 2.1; NHDES, 1996b). The PiscataquaRiver Basin has had as little as 45% ofrivers and streams supporting all uses(NHDES, 1990). In 1996, only 11 of 1001miles of freshwater rivers and streams inthe Piscataqua River Basin were partiallyor not supporting full use.

For all uses of New Hampshire’s openocean and coastal shoreline areas, onlyswimming restrictions were impairmentsfrom 1992 to 1996. This areas has sincehad shellfish harvesting closures

imposed. From 1992 to 1996, the coastalbasin and open ocean waters fully sup-ported all uses (Figure 2.2). Estuarieshave had large areas with classificationsthat reflect impaired use because ofrestrictions on shellfish harvesting due tothe presence of indicators of pathogens(Figure 2.2). Recent efforts to reclassifyshellfish waters have resulted inimproved use support in 1996. Indicatorsof pathogens also caused decreased sup-port for swimming in open ocean andcoastal shoreline areas from 1988-1992,while estuarine waters have had norestrictions on swimming.

Whole effluent toxicity tests decreaseduses of some coastal tributaries in 1992,and the presence of elevated metal con-centrations decreased use support intidal waters in 1994. Metals also impaireduse of some freshwater streams in 1996.Aquatic life support was impaired in theLamprey River in 1994 because of metals(NHDES, 1994). Only 4.4 square miles ofestuarine waters supported aquatic life

24

Hampton Beach

25

NEW HAMPSHIRE

Wastewater Treatment Plants (WWTP) Receiving watersNH0020966 Wallis Sands, Rye Atlantic OceanNH0100196 Newmarket Lamprey RiverNH0100234 Portsmouth Piscataqua RiverNH0100251 Rollinsford Salmon Falls RiverNH0100277 Somersworth Salmon Falls RiverNH0100455 Durham Oyster RiverNH0100609 Rockingham County Complex (prison) Ice Pond BrookNH0100625 Hampton Tide Mill CreekNH0100668 Rochester Cocheco RiverNH0100676 Milton Salmon Falls RiverNH0100692 Epping Lamprey RiverNH0100854 Farmington Cocheco RiverNH0100871 Exeter Squamscott RiverNH0101028 Star Island Conference Center Atlantic OceanNH0101141 Newington Piscataqua RiverNH0101192 Newfields Squamscott RiverNH0101303 Seabrook Atlantic OceanNH0101311 Dover Piscataqua RiverNHG640006 Swains Lake Village Water District Swains Lake via wetland

IndustryNH0000469 Tillotson Healthcare Co., Rochester Salmon Falls RiverNH0001091 KJ Quinn & Co., Inc., Seabrook Cains BrookNH0001490 Simplex Piscataqua RiverNH0001503 Bailey Corp. Hunts Island CreekNH0020923 Little Bay Lobster Piscataqua RiverNH0022306 Morton International, Seabrook Cains BrookNH0022055 EnviroSystems-Hampton Taylor RiverNH0022985 Aquatic Research Organisms Taylor RiverNH0090000 Pease Piscataqua RiverNHG250317 GE Somersworth Salmon Falls River

Power PlantNH0001601 PSNH Newington Station Piscataqua RiverNH0001473 PSNH Schiller Station Piscataqua RiverNH0020338 Seabrook Station Atlantic Ocean

Water Treatment PlantNH0000884 Portsmouth (Madbury) Johnson CreekNH0001031 UNH Oyster RiverNHG640007 Newmarket Lamprey/Piscassic rivers

MAINE

Wastewater Treatment Plants (WWTP) Receiving watersME0101397 Berwick Sewage District Salmon Falls RiverME0100285 Kittery Piscataqua RiverME0100820 South Berwick Sewer District Salmon Falls River

IndustryME0000868 Portsmouth Naval Shipyard, Dry docks Piscataqua RiverME0022861 Pratt & Whitney Great Works RiverME0022985 Watts Fluidair, Corp., Kittery Wilson Creek

National Pollutant Discharge Elimination System (NPDES) permitted sites in coastal NewHampshire area for which monitoring data are available in the Permit Compliance Systemdatabase.

TABLE 2.1

use in 1996, the other areas only partial-ly supported aquatic life because of ele-vated levels of PCBs in lobster tomalley(NHDES, 1996b). Overall, none of theestuarine water supported full usebecause of either PCBs or pathogens.Recreational uses and fish consumptionwere fully supported in all estuarinewaters. The health advisory for lobstertomalley is probably the result of histor-ical PCB contamination, and the re-clas-sification is based on studies conductedin the late 1980s and early 1990s (Isazaet al., 1989; Schwalbe and Juchatz,1991).

Septic systems, land disposal of solidwastes, stormwater runoff, CSOs andpoint sources have been the most com-mon suspected sources cited in 305(b)reports for non-support, although theestuarine sources of the PCBs responsi-ble for the lobster consumption advisoryare unknown. The presence ofpathogens, indicated by the presence ofelevated concentrations of fecal indicatorbacteria, has been the most commonpollutant. Other problem pollutants andconditions have been in-stream toxicity,low dissolved oxygen, ammonia andmetals. The trends presented in the twofigures reflect to a great extent the evolv-ing program of assessment.

The State of New Hampshire regu-lates point sources primarily through theNational Pollutant Discharge EliminationSystem (NPDES). Dischargers arerequired to obtain discharge permitsand the discharge has to meet set limits.The permitted dischargers in NewHampshire and Maine are listed in Table2.1. Sites are categorized as wastewatertreatment facilities (WWTFs), industriesor power plants. There are 19 WWTFs,ten industries and three power plantspermitted dischargers in coastal New

Hampshire waters, and three WWTFsand three industry permittees in Mainethat discharge into the waters of theGreat Bay Estuary.

The NPDES program is a source fora limited range of general contaminantdata in point source effluent. Monitoredpermit data are available from the Per-mit Compliance System database whichis maintained by the USEPA. TheNHDES and the USEPA both get reportsfrom permittees and act on violations,should they occur. A review of data for1996 at all permitted sites in Table 2.1showed violations of bacterial indicatorlimits were frequent at some sites andwere always met at other sites. Onlyrare violations of limits for discharges ofmetals occurred. Various toxicity assaysare used on effluent at most facilitiesother than some power plants. Somefacilities had no violations while othershad occasional violations of toxicity lim-its. Two WWTFs in New Hampshire hadproblems with meeting ammonia dis-charge limits.

In general, the water quality incoastal New Hampshire has improved.The major factor has been improvedsewage treatment facilities capabilitiesfor eliminating microbial contaminantsfrom their discharges. However, bothmonitoring activities and the contami-nants measured have increased duringthe last ten years, resulting in identifica-tion of previously undocumented causesfor use limitations. These changes haveoccurred while loading characteristics,discharge permit requirements and con-taminant issues have changed to reflectevolving concerns. There is a continuingneed to identify and reduce or eliminatesources of pollutants that are presentlyresponsible for limitations on uses of thestate’s estuarine and coastal waters.

26

27

Humans are susceptible to diseasescaused by waterborne microorgan-

isms. Some viruses, bacteria and proto-zoa are human pathogens, and theirpresence in surface waters and shellfishis a public health threat. Some patho-genic microorganisms are present natu-rally in estuaries and coastal waters. Theecology of many of these indigenousmicroorganisms is not well understood,and their presence would be difficult tomanage. However, most waterbornepathogens of concern in northern NewEngland are of fecal origin and thus arenot natural inhabitants in estuarinewaters. These microbes are introducedinto coastal waters largely as a result ofhuman activities, and can thus theoreti-cally be controlled. Known anthro-pogenic sources include inadequatelytreated wastewater discharges, septicsystems, boat discharges, urban andagricultural runoff and sanitary landfills,although significant contamination canalso come from waterfowl and otherwildlife.

2.2.1 PATHOGENS, BACTERIAL FECAL INDICATORS AND WATER QUALITY STANDARDS

The State of New Hampshire, alongwith every other jurisdiction that has theneed to assess water quality and classifywaters, uses bacterial indicators of fecal

contamination to assess the sanitaryquality of water. The number of potentialfecal-borne pathogens, both bacterialand viral, are too numerous and difficultto measure on a routine basis. NewHampshire presently uses fecal coliformsfor shellfish growing waters, as recom-mended by the National Shellfish Sanita-tion Program (NSSP, 1995). Forrecreational uses of marine and estuarinewaters, enterococci are used, andEscherichia coli is used for freshwaterrecreational uses, both as recommendedby the U.S. EPA. The bacterial indicatorstandards for classifying surface waters inNew Hampshire are summarized inTable 2.2. These indicator bacteria havebeen chosen as the best indices of fecalcontamination for the different purposesbased on numerous studies. In manystudies conducted by UNH/JEL, Clostrid-ium perfringens is also included as anindicator of long-term fecal contamina-tion and contamination associated withresuspended sediments. The following isa summary of information on the statusand trends of these indicator bacteria,with some limited information on actualbacterial pathogens and viruses. Becauseof the extensive amount of data for thenumerous bacterial indicators that havebeen used, fecal coliform data will beused for most illustrations of spatial andtemporal trends.

2.2

STATUS AND TRENDS

OF MICROBIAL PATHOGENS AND

FECAL INDICATORS

Geometric Mean GMC Maximum Limit MLCSurface water Classification Indicator Concentration* # of samples Concentration* Frequency

Freshwater Class A Escherichia coli 47 3 in 60 days 153 1 of 3 samplesFW designated beach Class A Escherichia coli 47 3 in 60 days 88 1 of 3 samplesFreshwater Class B Escherichia coli 126 3 in 60 days 406 1 of 3 samplesFW designated beach Class B Escherichia coli 47 3 in 60 days 88 1 of 3 samples

Tidal Recreational enterococci 35 3 in 60 days 104 1 of 3 samples

Shellfish-growing Approved Fecal coliforms 14 30 (most recent) >43 <10% of samplesRestricted Fecal coliforms 14-88 30 (most recent) >260 <10% of samplesProhibited Fecal coliforms >88 30 (most recent)

* Concentrations per 100 ml

Bacterial indicator standards for surface water classification: freshwater, tidal recreational watersand shellfish-growing waters.

TABLE 2.2

2.2.1.1 Spatial Distribution

The spatial distribution of bacterial indi-cators in coastal New Hampshire hasbeen relatively well documented in mostareas. Adequate spatial coverage of sam-pling is necessary to aid in the identifica-tion of contaminant sources and todocument the effects of efforts to reducepollution sources. In general, bacterialcontaminants are present at higher con-centrations in tributaries in comparisonto the main estuarine waters (Great Bay;Hampton Harbor) and the AtlanticOcean. This is a function of the mostimportant sources of contaminants beingpresent upstream and along the shore-lines of the tributaries, the smaller vol-umes of water in tributaries having lesscapacity for favorable dilution impactson contaminant concentrations, and con-taminants are subject to physical and bio-logical processes that remove them fromwater as a function of time, distance andchanging environmental conditions dur-ing transport through the tributaries tothe main water bodies.

Early data on bacterial contaminationcan be found in Jackson (1944). Thesedata reflected the high concentrationloading of untreated sewage into thetributaries to Great Bay Estuary, all ofwhich had average total coliform con-centrations of >800 /100 ml, with aver-ages ranging from 803 to 9,020/100 ml.Concentrations were much lower atsites in Great and Little bays, butremained elevated compared to morerecent data, ranging from 20 to 144/100ml and generally in excess of the limitof 70 total coliforms/100 ml for shell-fishing. In 1974, the New HampshireWater Supply and Pollution ControlCommission (NHWSPCC) reportedmedian total coliform concentrationsranging from 50/100 ml at an upstreamsite in the Exeter River to 109,000/100ml at an upstream site in the CochecoRiver in freshwater tributaries(NHWSPCC, 1975). In tidal waters, con-centrations were <21/100 ml at Hamp-ton Harbor, the Atlantic coast areas andin the Bellamy River, but ranged up to307,000/100 ml in the Cocheco River.

State agencies have conducted routinemonitoring of coastal waters for over 30years. Freshwater sites are monitored byNHDES, with NHDES, NHDHHS andNHF&G monitoring tidal waters. Citizenvolunteers have also been involved inmonitoring microbial water quality in thecoastal waters. The Great Bay Watch hasmonitored fecal coliforms at up to 24sites in the Great Bay Estuary for over tenyears (Reid et al., 2000). UNH and JELhave contributed substantial water quali-ty data as a result of numerous studiesthroughout coastal New Hampshire.

Great Bay and Upper Little Bay withSquamscott/Exeter and Lamprey Rivers

This area extends from the dams on thetwo rivers through all of Great Bay andupper Little Bay to Fox Point and thearea south of the mouth of the OysterRiver (Figure 2.3). The most spatiallyand temporally intensive database forbacterial contaminants in Great Bay isthe NHDHHS shellfish water monitoringprogram database. The data for 12 of theNHDHHS sampling stations (Figure 2.3)were reviewed and interpreted as part ofthe 1995 sanitary survey for theapproved shellfishing areas in Great andLittle bays (NHDHHS, 1995; Jones andLangan, 1995b). Fecal coliform concen-trations were low enough to support anapproved classification for much ofGreat Bay, although elevated concentra-tions near the mouths of the Lamprey,Squamscott, Oyster and Winnicut riversonly supported restricted or prohibitedclassifications. Major rainfall events hadsignificant negative effects on waterquality throughout the area and werenoted as a potential condition for classi-fication. The area near the mouths of theSquamscott and Lamprey rivers hasrecently been subject to more detailedmonitoring to better define the bound-ary between restricted and approvedclassifications. Dye studies for theDurham and Newmarket wastewatertreatment facilities (WWTFs) plus theGreat Bay Marina have been conducted,and the results will provide needed datato better define safety zones in areas

28

29

Miles0.5 0.25 0 .5

Kilometers.5 0 .5

Great Bay Watch Sites

NHDHHS Sampling Sites

NHDES Sampling Sites

UNH/JEL Sites

FIGURE 2.3

Great Bay, Upper Little Bay,

Squamscott/Exeter Riverand Lamprey River

water quality sampling region.

around the mouths of the Lamprey andOyster rivers and in Little Bay.

The long-term Great Bay NationalEstuarine Research Reserve (GBNERR)monitoring program has provided aneleven year database for fecal coliforms,enterococci, E. coli and C. perfringens atAdams Point between Great and Littlebays, Chapmans Landing in the Squam-scott River and at the Town Landing onthe Lamprey River (Langan and Jones,2000; Langan and Jones, 1997). In 1996-97 as in 1988-97, fecal coliform, E. coli,enterococci and C. perfringens concen-trations were lowest at Adams Point atboth high and low tides (Figures 2.4 and2.5; Appendix G). Most indicators havebeen present at relatively low concentra-tions in the Squamscott River at high tide,whereas at low tide contaminant con-centrations have been much higher. Thelarge difference in contaminants in theSquamscott River is a result of dilutionwith less contaminated bay water at hightide. Bacterial indicators in the LampreyRiver are present at elevated concentra-tions at both high and low tides. Similarobservations, i.e., elevated bacterial lev-els in the Lamprey River compared toother areas in Great Bay at both high and

low tide, have been reported by theGreat Bay Watch (Reid et al., 2000). TheTown Landing area appears to be signif-icantly affected by undefined localizedconditions that are currently under inves-tigation by state agencies.

The water quality in the tributaries toGreat Bay has been assessed as part ofnumerous other studies. Both the Lam-prey and Squamscott rivers were part ofa three year project to investigate theeffects of storm events on water qualityin all tributaries (Figures 2.6 and 2.7) tothe Great Bay Estuary (Jones and Lan-gan, 1994a; 1995a; 1996a). An analysis ofall three years can be found in Jones andLangan (1996a). The geometric meanfecal coliform (FC) concentrations wererelatively low during dry weather overthe three year study at the freshwatersites just above the dams on both theLamprey (9 FC/100 ml) and the Squam-scott (31 FC/100 ml) rivers (Figure 2-6).Compared to the freshwater sites, theconcentration at the tidal water siteswere lower in the Squamscott (23 FC/100ml) and higher in the Lamprey (48FC/100 ml) during dry weather. Concen-trations increased significantly at all foursites during storm events (Figures 2.6

30

Feca

l col

iform

s/10

0 m

l

1988-89 1989-90 1990-91 1991-92 1992-93 1993-94 1994-95 1995-96 1996-97

0

100

200

300

400

500

600

Adams Point

Squamscott River

Lamprey River

FIGURE 2.4 Temporal trends for fecal coliforms (colonies/100 ml) at three sites in the Great Bay Estuary at low tide.

31

and 2.7). During the same years, fecalcoliform concentrations in the Squam-scott River downstream of the dam indowntown Exeter were generally>50/100 ml (Reid et al., 2000). Fecal col-iform concentrations in the WinnicutRiver have been elevated compared tomost other sites in Great Bay at low tide,but are diluted to low concentrations athigh tide (Reid et al., 1998). The smalltributaries that flow into the WinnicutRiver and the southeast corner of GreatBay were sampled during 1994-95 (Jonesand Langan, 1995b). Despite some ele-vated concentrations of fecal coliforms,the tributaries appeared to have littleimpact on water quality in Great Bay.

Both the tidal and freshwater portionsof the Squamscott/Exeter River water-shed were studied in detail during 1994-95 (Jones and Langan, 1995c). Along themain channel of the Squamscott River,concentrations of fecal coliforms and E.coli increased dramatically goingupstream from Chapmans Landing to theExeter WWTF discharge pipe. Bacterialcontaminants were present in relativelyhigh concentrations in some of the fif-teen small tributaries sampled along theSquamscott River, and analysis of salini-

ties and bacterial contaminants suggest-ed that the tributaries were affectingcontaminant concentrations betweenChapmans Landing and the upperreaches of the tidal river. However, therewas no evidence for significant influenceon water quality by any one tributary onthe Squamscott River. Samples collectedfrom ten sites in the freshwater ExeterRiver and tributaries showed higher con-centrations in the downstream area neardowntown Exeter. In a follow-up study,bacterial concentrations in the freshwa-ter tributaries to the Exeter and Squam-scott rivers were found to be elevatedabove state standards during dry andwet weather, with more severe contami-nation during wet weather (NHOSP,1995a). The sites with higher concentra-tions in the lower portions of the ExeterRiver close to downtown Exeter wereaffected by stormwater runoff, and weresuspected to be affected by septic sys-tems and agricultural runoff (Becker andRadacsi, 1996).

An earlier study focused on the areafrom the Exeter River dam to AdamsPoint during 1989-90 (Jones, 1990). Priorto February, 1990, elevated bacterial con-centrations in the Squamscott River were

0

50

100

150

200

250

300

1988-89 1989-90 1990-91 1991-92 1992-93 1993-94 1994-95 1995-96 1996-97

Feca

l col

iform

s/10

0 m

l

Adams Point

Squamscott River

Lamprey River

Temporal trends for geometric means of fecal coliforms (colonies/100 ml) at three sites in FIGURE 2.5the Great Bay Estuary at high tide.

32

Fecal coliforms/100 ml

Wet Weather

Dry Weather

64

23

173

4831 7 31 10

272

79

150

30

Exeter River Lamprey River Oyster River Bellamy River Cocheco River Salmon Falls River

FIGURE 2.7 Geometric mean fecal coliforms (colonies/100 ml) in water collected during dry weather and storm events for three consecutive years in tributaries to the Great Bay Estuary: 1993-96, tidal water.

Fecal coliforms/100 ml

Wet Weather

Dry Weather

Exeter River Lamprey River Oyster River Bellamy River Cocheco River Salmon Falls River

221

3143 9

312

26

149

33

550

133

87

39

FIGURE 2.6 Geometric mean fecal coliforms (colonies/100 ml) in water collected during dry weather andstorm events for three consecutive years in tributaries to the Great Bay Estuary: 1993-96, freshwater.

33

dominated by discharges from the ExeterWWTF. Water quality in the SquamscottRiver and Great Bay improved followingthe upgrading of the facility in early1990. The concentrations of fecal col-iforms, E. coli and enterococci dis-charged from the WWTF were high(105-106/100 ml) prior to the upgrade,and decreased to low levels (< 4/100 ml)thereafter. A comparison of indicatorsdemonstrated the misleading nature ofthe total coliform assay. The organismsdominating a positive test value of 3000total coliforms/100 ml in effluent collect-ed after the upgrade when other indica-tor concentrations were nondetectablewere identified as Hafnia, Citrobacterand Aeromonas sp., all common envi-ronmental species not associated withfeces. These data were used as part ofthe justification by the state to discontin-

ue use of total coliforms as an indicatorof fecal contamination in surface waters.

Oyster and Bellamy Rivers and Lower Little Bay

This area extends from the freshwaterportions of the two rivers through thetidal portions and into Little Bay from FoxPoint to the General Sullivan Bridge (Fig-ure 2.8). In the Oyster River, the DES andDHHS database results have been aug-mented by more detailed UNH studies(Jones and Langan, 1994c; 1993a; Mar-golin and Jones, 1990) and a recent studyby NHCP (NHCP, 1996). NHDHHS datafor 12 sampling stations in and aroundGreat and Little bays were reviewed andinterpreted as part of the 1995 sanitarysurvey (NHDHHS, 1995; Jones and Lan-gan, 1995b). Fecal coliform concentra-tions were low enough to support an

1

9

17

Miles0.5 0.25 0 5

Kilometers.5 0 .5

Great Bay Watch Sites

NHDHHS Sampling Sites

NHDES Sampling Sites

UNH/JEL Sites

FIGURE 2.8

Oyster River, Bellamy River and Lower Little Bay water quality sampling region.

34

approved re-classification for the area inLittle Bay that was monitored, whichincluded two new sites during 1995-96near Mathes Cove and Langley Island.Elevated concentrations near the mouthof the Oyster River only supported arestricted classification. Major rainfallevents had significant negative effects onwater quality and were noted as a poten-tial condition for classification. Dye stud-ies for the Durham WWTF and for theGreat Bay Marina, conducted by USEPAin 1996 and 1997 (reports in preparation),will provide needed data to better definesafety zones around these sites.

A new sanitary survey focused moreintensive monitoring, including four newsites, in lower Little Bay (NHDHHS,1998). Sanitary survey work was also per-formed in the Bellamy River and theanalysis of fecal coliform data has beenpublished (Jones, 1998a). The shorelinesurvey and fecal coliform concentrationsat five of the six sites were consistentwith an approved classification of muchof lower Little Bay. Initially, only an areaaround Broad Cove was classified asapproved, as other areas required addi-tional samples. In June, 1998, as part ofan amendment written to the originalsanitary survey, most of the rest of lowerLittle Bay was re-classified as approved,except for an area from the mouth of theOyster River east to Fox Point and areasaround the two marinas.

Margolin and Jones (1990) found ele-vated concentrations of bacterial indica-tors in the Town Landing area of theOyster River, especially following rainfallevents. Geometric mean fecal coliformconcentrations were >14/100 ml at sixsites along the length of the river, exceptthe WWTF outfall which had residualchlorine that disinfected the effluent andthe river at the pipe. Poliovirus was alsodetected in 10 of 60 samples at six sitesin the Oyster River, suggesting thatsewage-borne viral pathogens could bepresent. There was no relationshipbetween viral detection and concentra-tions of bacterial indicators.

The Oyster River Nonpoint SourcePollution Assessment project presented acomprehensive assessment of nonpoint

source pollution in the Oyster Riverwatershed, with emphasis on the tidalportion of the river and the tributariesthat empty directly into the tidal river(Jones and Langan, 1993a). Fecal-bornebacteria levels were elevated in thewatershed, and the levels in the tidal areawere as high or higher than measure-ments made in other tidal rivers in theGreat Bay Estuary. The geometric meanfor fecal coliforms for all tidal sites was37 FC/100 ml, which is consistent with arestricted or conditionally approvedshellfish harvesting classification.

Fecal coliform and enterococci con-centrations were highest in the TownLanding area, in Mill Pond and upstreamin the tidal tributaries. Extensive samplingin the Beards and Johnson Creek water-sheds showed elevated concentrations ofbacteria throughout these watersheds.The bacterial contamination was dominat-ed by nonpoint sources suspected to beon-site private sewage disposal systems(OSDs) and associated groundwater flow,urban and agricultural surface runoff, andother as yet undetermined sources. Theevidence for these sources was based onelevated bacterial and nutrient contami-nation in some areas (Deer Meadow andBeards creeks) of the shoreline of thetidal river (suspected source: OSDs),areas within some tributaries where nodirect source is apparent (suspectedsources: groundwater flow, wildlife), con-sistent elevated responses to rainfall/runoff, and site-specific sampling arounda farm where horses graze in and arounda tributary. However, there is also someevidence to suggest that the DurhamWWTF and some sewer lines are inter-mittent sources of significant contamina-tion in water bodies that are crossed bysewer pipes.

The JEL study was continued for a sec-ond year, with more emphasis on theJohnson and Beards Creek watersheds(Jones and Langan, 1994c). Fecal col-iforms, enterococci and C. perfringensconcentrations were measured at fifteensites along the tidal portion of the OysterRiver. The highest concentrations wereagain detected in the upper reaches ofthe river near the Town Landing, with

35

decreased fecal coliform and enterococciconcentrations near the WWTF outfallcaused by residual chlorine in the efflu-ent. C. perfringens concentrations werehighest near the WWTF outfall becausetheir spores are resistant to chlorine dis-infection. Elevated concentrations of bac-terial indicators were again measured inthe two watersheds, and a detailed studyof salinity and fecal coliforms suggeststhat mixing of high concentrations infreshwater with cleaner salt waterreduces bacterial concentrations in waterbeyond dilution effects. Expansion ofsample sites into some branch brooks inthe Johnson Creek watershed showedhigh concentrations around some hous-ing developments that depend on septicsystems, with one site contaminated byan identifiable residential septic system.In the more urban Beards Creek water-shed, houses still on septic systems orleaky sewer lines were probably thesources of bacterial contamination. Infact, a small study at the mouth of BeardsCreek gave clear evidence of contamina-tion from a sewer line that crosses themudflat. The latter and other identifiedsources of bacterial contaminants havebeen investigated by NHDES.

In a more recent study, data support-ed conclusions that the lower portion ofthe Oyster River watershed arounddowntown Durham is where most con-tamination occurs (NHCP, 1996). Thisstudy included sampling sites in theupper portions of the watershed and inthe College and Pettee Brook areas thatwere not included in the JEL studies.Septic systems/leaky sewers and urbanand agricultural runoff were probably themain sources of bacterial contamination.Sampling at most sites during stormevents showed elevated bacterial con-centrations, often exceeding 100 E.coli/100 ml, and sometimes exceeding1000/100 ml for some sites.

Samples were collected at sites in thefreshwater and tidal areas of the Bellamyand Oyster rivers as part of a three-yearstudy to investigate the effects of stormevents in tributaries to the Great BayEstuary on water quality in the estuary(Jones and Langan, 1996a). The geomet-

ric mean concentrations of fecal coliformwere relatively low during dry weatherover the three year study at freshwatersites in both the Oyster (26/100 m) andthe Bellamy (33/100 ml) rivers (Figure2.6). The concentration in the tidalwaters were low in both rivers (<11/100ml) during dry weather (Figure 2.7).Concentrations increased significantly atall four sites, especially the freshwatersites, during storm events.

Salmon Falls, Cocheco, and (Upper) Piscataqua Rivers

This area includes all estuarine and asso-ciated freshwater waters north of whereLittle Bay and the Piscataqua River meetnear Dover Point (Figure 2.9). In theupper Piscataqua, Cocheco and SalmonFalls rivers, the DES and DHHS databas-es are augmented by some UNH studies,as well as State of Maine and SpinneyCreek Shellfish Co. monitoring results(Mitnick and Valleau, 1996; Livingston,1995). Sites in the freshwater and tidalareas of the Cocheco and Salmon Fallsrivers were studied as part of the three-year investigation on storm events intributaries to the Great Bay Estuary(Jones and Langan, 1996a). The geomet-ric mean fecal coliform concentrationswere elevated compared to other tribu-taries during dry weather over the threeyear study at freshwater sites in both theCocheco (87 FC/100 ml) and the SalmonFalls (39 FC/100 ml) rivers (Figure 2.6).The concentration in the tidal waterswere low in the Salmon Falls (30 FC/100ml) and high in the Cocheco (79 FC/100ml) during dry weather (Figure 2.7).Concentrations increased significantly(all >100 FC/100 ml) at all four sites,especially at the freshwater sites, duringstorm events. Some attenuation of bacte-rial concentrations apparently occursbetween the upper and lower tidal por-tions of the Cocheco River, based onsamples collected during 1997 (Reid etal., 1998). Even lower concentrationswere measured downstream in the Pis-cataqua River. Lower bacterial concen-trations were measured at a moreupstream site in the Cocheco River. Thehigh concentrations of bacteria in the

downtown and downstream portions ofthe river suggest that urban areas ofDover are major sources of contami-nants to this area of the Estuary, espe-cially during storm events.

More recent studies have focused oncontaminants in storm drains in down-town Dover and Exeter (Jones et al.,1999; Jones, 1998). All of the drains haddetectable microbial contaminants dur-ing dry and wet weather. Levels of con-taminants in street runoff were relativelylow, suggesting that sources within thestormdrain system, probably illicit con-nections and leaking sewer pipes, werethe major sources of the microbial con-taminants. Contaminant concentrations

in the Cocheco River were relativelylower during wet and dry weather com-pared to previous (Jones and Langan,1996a) data.

Studies that focused on indigenousbacterial pathogens (i.e., vibrios) includ-ed assessments of fecal-borne bacteria(Jones et al., 1991a; O’Neill et al., 1990).Relatively high concentrations of fecalcoliforms were detected in the SalmonFalls and Piscataqua rivers compared toPortsmouth Harbor during 1989-92. Thegeneral trend of higher concentrations offecal-borne bacteria in tributaries wasdirectly related to incidence of Vibriovulnificus detection, but not for Vibrioparahaemolyticus.

36

Great Bay Watch Sites

NHDHHS Sampling Sites

NHDES Sampling Sites

Miles0.5 0.25 0 5

Kilometers.5 0 .5

UNH/JEL Sites

Gulfwatch/NHDES Sites

FIGURE 2.9

Salmon Falls, Cochecoand upper Piscataquarivers water quality sampling region.

37

Portsmouth and Little Harbors and Lower Piscataqua River

This area includes the Piscataqua Riversouth of Dover Point, The Back Channelarea and Portsmouth and Little harbors(Figure 2.10). In Portsmouth Harbor, Lit-tle Harbor, Back Channel and the lowerPiscataqua River, routine NHDHHS andNHDES monitoring provides the mostconsistent databases, along with somelimited UNH/JEL data. The data from theNHDHHS database have been summa-rized and interpreted relative to shellfishwater classification standards in Jonesand Langan (1996c), and more recentdata are available (Appendix G). Sites inLittle Harbor were generally in support of

an approved classification, while fecalcoliform concentrations were relativelyhigh in Back Channel and tributary sites.Some areas in the Back Channel willprobably be within a closed safety zonein the area around the PortsmouthWWTF effluent pipe.

A spatially intensive monitoring pro-gram to determine fecal contaminationlevels in water around Portsmouth Har-bor, including some sites on the NewHampshire side, was conducted during1992-93 (Jones, 1994). The sites werelocated along the main channel of thePiscataqua River. The geometric meansfor enterococci in the study area waterswere generally consistent with safe recre-ational use criteria set by Maine and New

Great Bay Watch Sites

NHDHHS Sampling Sites

NHDES Sampling Sites

Miles0.5 0.25 0 .5

Kilometers.5 0 .5

Gulfwatch/NHDES Sites

FIGURE 2.10

Portsmouth and Little Harbors and

lower Piscataqua Riverwater quality

sampling region.

Hampshire (geometric mean <35/100ml). The geometric means for fecal col-iforms were all lower than the limit of 14fecal coliforms/100 ml for approvedshellfish-growing waters, but the fre-quency of samples greater than 43/100ml was greater than 10% at the 6 stations.A long-term database (monthly for tenyears) for samples from Ft. Constitutionin New Castle has shown concentrationsof fecal indicator bacteria to be consis-tently low at the mouth of the river (Dr.S. Jones, unpublished data). Four sites inNorth and South Mill ponds have beenmonitored for fecal coliforms saince 1997by the Great Bay Coast Watch (Reid etal., 2000). Two one-year studies in NorthMill Pond included fecal coliform meas-urements of the pond and storm drains(Jones, 2000; ANMP, 1998).

Rye Harbor and Coastline

This area includes the coastal areas fromLittle Harbor south to Hampton Harbor(Figure 2.11). In Rye Harbor and thecoastline, existing data are mostly fromNHDHHS and NHDES monitoring pro-grams. Some of the data from the NHD-HHS database have been summarizedand interpreted relative to shellfish waterclassification standards in Jones and Lan-gan (1996c), and more recent data arealso available (Appendix G). NHDHHSdata for some additional sites in tributar-ies are not presented, and NHDHHS dataare summarized in Appendix G. Thegeometric mean concentrations of fecalcoliforms at all four sites were <14/100ml. However, the incidence of samples>43/100 ml was in excess of 10% in the

38

NHDHHS Sampling Sites

1Miles

.5 0 1

Kilometers1 .5 0 1

FIGURE 2.11

Coastal New Hampshire,from Little Harbor to theMassachusetts border,water quality samplingregion.

39

last 30 samples at all but an inner harborsite, suggesting non-random contamina-tion events are too frequent in the harborto allow approved shellfish classification(NSSP, 1995). A boat pumpout facility hasrecently been put in at the NH Depart-ment of Resources and Economic Devel-opment (DRED) dock.

Hampton Harbor and Tributaries

This area includes all of theHampton/Seabrook Estuary and tributar-ies (Figure 2.12). In Hampton Harbor,routine NHDHHS and NHDES monitor-ing, in cooperation with NHF&G, hasprovided long-term databases, whilesome recent more detailed UNH/JELstudies provide added information (Lan-gan and Jones, 1995 a&b). The NHDHHSdata for sites currently used for classify-

ing shellfish waters in Hampton Harborhave been reviewed and interpreted(NHDHHS, 1994a), and more recent dataare presented in Appendix G. The geo-metric mean fecal coliform concentra-tions for all ten sites were <14/100 ml.However, the incidence of concentra-tions >43/100 ml exceeds the standard10% at some sites. Some of the sites withthe more frequent incidence of high con-centrations are near the mouth of MillCreek on the west shore, suggesting thatcontamination from the creek may beinfluencing water quality in the area.Improved water quality in recent yearshas resulted in a recent upgrading of theshellfish harvest classification of the largeMiddle Ground clam flat in Seabrookfrom restricted to conditionally approved(NHDHHS, in prep.).

NHDHHS Sampling Sites

Miles0.25 0 0.25

Kilometers0.25 0 0.25

FIGURE 2.12

Hampton Harbor andtributaries water quality

sampling region.

A two-year study on septic systems inSeabrook included some surface watermonitoring, with emphasis on tributariesthat border residential areas (Jones et al.,1995; 1996). Samples were collectedfrom 16 sites at low tide in Mill Creek,Farm Brook, some tidal creeks and theharbor. Water from Mill Creek had thehighest levels of indicator bacteria (<200FC/100 ml) during sampling in 1995 and1996. Concentrations of bacteria detectedat all upstream tributary sites were ele-vated compared to harbor sites. Lowerconcentrations in the harbor were prob-ably the result of dilution and die-off inthe more saline waters, which representsless favorable conditions for bacterialsurvival. Seven sites, mostly in tributaries,did not meet the New Hampshire swim-ming water standard of 35 enterococ-ci/100 ml. Based only on the study data,only one site had a mean fecal coliformconcentration <14/100 ml. There was noclear relationship between groundwatercontamination and surface water qualityat any site, although the elevated con-centrations of bacteria in streams nearhigh density residential areas suggestsseptic systems are a likely source of con-tamination. During 1996-97 when septicsystems were being disconnected andsewage was diverted to the new treat-ment facility, measurements of contami-nants in the surface waters of the harborand tributaries showed little change fromprevious years (Jones, 1997).

Clearly, there are sources of bacterialcontaminants that persist in all areas of

coastal New Hampshire and limit uses ofestuarine and coastal waters. The con-cern is the protection of public health inareas that will only experience increasedhuman use in the future. Continuedefforts to identify and either eliminate oreffectively manage the impacts of fecalcontamination sources is an important,on-going issue in coastal New Hamp-shire. As the next section suggests, waterquality in general has improved over thelast ten years, but the widespread natureof the problem suggests that muchremains unknown about the issue.

2.2.1.2 Temporal Trends

There appear to be some general tempo-ral trends that have occurred in manyareas of the Seacoast. Fecal-borne bacter-ial contaminant concentrations havedecreased in all coastal waters since theearly 1990s as a result of the extensiveimprovements to wastewater treatmentfacilities. Bacterial contaminants are alsogenerally present at higher concentrationsat low tide compared to high tide, mostlyas a function of mixing of more contami-nated freshwater with cleaner tidal water.Bacterial concentrations are often elevat-ed during autumn and winter comparedto other seasons in some areas. Thisobservation is probably related both tothe amount of runoff associated with rain-fall events as a function of seasonal dif-ferences in evapotranspiration andinfiltration, and to the enhanced survivalof bacterial contaminants with colderwater temperatures (Jones et al., 1997).The most severe incidences of elevatedcontamination occur in temporally lesspredictable conditions, i.e., following rain-fall/runoff events and upsets in treatmentprocesses at WWTFs. In addition, >100year storms such as the one that occurredin October, 1996, tax the capacities ofmost WWTFs because of infiltration intothe sewer systems and overloading oftreatment plants. Some areas are moreprone to contamination incidencesbecause of proximity to WWTFs, espe-cially those that may lack effective controlmeasures for stormwater runoff and haveless capacity for effective wastewatertreatment during storm events.

40

Water quality survey on Cocheco River

41

Certain sites in coastal New Hamp-shire have been sampled for decadesand the results can be used for deter-mining temporal trends. Data from threereports (Jones and Langan, 1996a;NHWSPCC, 1975; NHWPC, 1960) aresummarized in Table 2.3 to illustrate thedramatic improvements in water qualitysince 1960. Because the two earlierreports used total coliforms and the thirdused fecal coliforms, it was assumed thattotal coliform concentrations were equiv-alent to five times the fecal coliform con-centrations, and the 1996 data wereconverted to total coliform equivalentdata. This conversion is based on therelationship between total and fecal col-iform standards for classifying shellfishgrowing waters (NSSP, 1995). The datashow decreases in total coliform concen-trations in all six rivers from 1960 to

1996. The decrease was most dramatic inthe Cocheco River, which has remainedthe most contaminated tributary since1944, but which showed a nearly 100-fold decrease from 1975 to 1996. Thehigher concentrations in 1975 comparedto 1960 may reflect increased loading ofwastewater treatment facilities due to thenearly doubling (158,800 to 275,800) ofpopulations in Rockingham and Straffordcounties from 1960 to 1980 (NHOSP,1997a). There was also a dramatic,steady decrease in the Exeter/SquamscottRiver and a less extensive decrease in theSalmon Falls River (Figure 2.13). The fol-lowing section summarizes in moredetail existing information on the tempo-ral trends of bacterial contamination inthe different estuarine and coastal areasof New Hampshire. Where possible, dis-cernable temporal trends are related to

FRESHWATER SITES AT TIDAL DAMS

Exeter R. Lamprey R. Oyster R. Bellamy R. Cocheco R. Salmon Falls R.YEAR 9-EXT 5-LMP 5-OYS 5-BLM 7-CCH 5-SFR

1960 19700 524 656 — 16540 42661975 5044 1088 3742 4786 133690 42661996* 1490 350 1310 1345 1530 1475

*1996 data transformed by multiplying fecal coliform concentrations by 5.

Long-term trends for total coliform concentrations (per 100 ml) in water samples collected fromsix tributaries to the Great Bay Estuary, 1960, 1975, and 1996.

TABLE 2.3

Squamscott River

Salmon Falls River

0

5000

10000

15000

20000

1960 1975 1996

Total coliforms (colonies/100 ml) in the Exeter/Squamscott and Salmon Falls rivers: 1960-1996. FIGURE 2.13

management efforts to reduce pollution.The overall trend over the nine year

period of GBNERR monitoring (Langanand Jones, 1997) has been a generaldecrease in bacterial contaminants at allsites (Figures 2.4 and 2.5), although con-centrations of all indicators were higherduring 1995-96 than during previousyears. The three-year study of tributariesto Great Bay Estuary also showed somebacterial contaminants were present atsignificantly higher concentrations during1995-96 compared to the previous twoyears in the Lamprey and Squamscottrivers (Jones and Langan, 1996a). Thelong-term decrease in bacterial concen-trations was most dramatic in the Squam-scott River, especially after 1990 whenthe Exeter WWTF was upgraded. Trendsfor fecal contaminants were less dramat-ic at other sites like Adams Point, whereconcentrations have been relatively low(<33 FC/100 ml) since 1988. It also

appears that reducing concentrationsmuch below the standard 14 FC/100 mlmay be difficult when other areas con-tinue to have higher concentrations. Sea-sonal trends show contaminants tend tobe present in higher concentrations dur-ing late autumn and winter, as illustratedin Figure 2.14 for enterococci at AdamsPoint from 1989-97, which is consistentwith runoff conditions and bacterial sur-vival patterns (Jones et al., 1997). As pre-viously mentioned, contamination trendsat the Lamprey River do not follow typi-cal patterns, as fecal coliforms are typi-cally highest during the summer, insteadof autumn/winter.

Various studies in the Oyster Riverwere conducted from 1992-1997 (Jonesand Langan, 1996a; 1994c; 1993a; Reid etal., 1998). The 1992-93 seasonal trendsfor enterococci showed a clear trend ofelevated concentrations in summer,while fecal coliform concentrations

42

0

20

40

60

80

100

1989 1990 1991 1992 1993 1994 1995 1996 1997

High Tide

Low Tide

FIGURE 2.14 Monthly concentrations of enterococci (colonies/100 ml) at high and low tides at Adams Point: 1989-1997.

43

exhibited a mixture of trends at all sites(Jones and Langan, 1993a). The nextyear, seasonal trends for enterococci andfecal coliforms were mixed, while C. per-fringens showed a clear trend of elevat-ed concentrations during springtime foralmost all sites (Jones and Langan,1994c). In the Johnson Creek watershed,fecal coliform and enterococci concen-trations were uniformly at much higherconcentrations during summer and, to alesser extent, autumn, compared to win-ter and spring. This may be the result ofincreased regrowth at higher tempera-tures and reduced flow during warmmonths. Rainfall events >0.25”/24 hcaused elevated concentrations of ente-rococci at most sites and higher fecal col-iforms at sites near the Town Landing.There has been an overall decrease infecal coliform concentrations near themouth of Bunker Creek from 1992-97(Reid et al., 1998). At Mill Pond, fecal col-iform and enterococci concentrationswere decreasing from 1993 to 1996 dur-ing both dry and wet weather (Jones andLangan, 1996a). In the Bellamy River,fecal coliform and enterococci concen-trations increased from 1993 to 1996 dur-ing both dry and wet weather.

In downtown Dover above the tidaldam, fecal coliform and enterococci con-centrations exhibited mixed trends from1993 to 1996 during both dry and wetweather (Jones and Langan, 1996a). Inthe tidal portion of the Cocheco River,fecal coliform and enterococci concen-trations increased from 1993 to 1996 dur-ing both dry and wet weather. Thetrends for both enterococci and fecal col-iforms were mixed for dry and wetweather at the freshwater and tidal sitesin the Salmon Falls River.

Temporal trends for fecal coliformsshowed an overall decrease in concen-trations since 1988, especially after 1991,in Portsmouth Harbor, Little Harbor, theBack Channel and the lower PiscataquaRiver (Figure 2.15). The striking decreaseafter 1991 was coincident with the con-struction of advanced wastewater treat-ment in Portsmouth. Continued detectionof fecal coliforms at concentrations>14/100 ml are the result of lingering

nonpoint sources and possibly the twoCSOs remaining in Portsmouth. The con-tribution of the CSOs to contaminantloading is not known, although the CSOsdischarge a combination of untreatedsewage and stormwater during somestorm events (NHDES, 1996a).

In Rye Harbor, concentrations of fecalcoliforms have decreased at all sitessince 1985, especially at the harbormouth (see Appendix G). Lower concen-trations after 1991 could have been theresult of connection of some Rye resi-dences to the Hampton WWTF.

The temporal trends for annual geo-metric mean fecal coliform concentra-tions in Hampton/Seabrook Harborshowed an overall decrease for all sitesfrom 1988 to 1996. The lowest concen-trations for 8 of the 10 sites occurred in1995. Further improvements in waterquality are expected to occur followingthe completion of connections of allpresent septic system sites in Seabrook tothe new town sewer system. Improve-ments in the sanitary quality of the Har-bor water was not yet apparent inmid-1997 after many of the areas adja-cent to tidal waters had been connected(Jones, 1997).

The overall improvement in waterquality relative to bacteriological meas-urements is a reflection of the significantresources expended to improve waste-water treatment facilities in coastal NewHampshire. Population growth continuesat a slower pace relative to previousdecades. The estimated increase in pop-ulation in Strafford and Rockinghamcounties from 1990 to 1996 was 350,000to 367,900, only a 5% increase (NHOSP,1997b). Nevertheless, increases in humanpopulation, development, impervioussurfaces with associated stormwaterrunoff, and wastewater treatmentdemands will continue to change theability of watersheds to handle the addi-tional pollution. A better understandingof the watershed factors that affect trans-port and fate of microbial contaminantswould help frame effective strategies foreliminating or managing pollutionsources and transport pathways for thesecontaminants to estuarine waters.

2.2.2 SOURCES OF FECAL-BORNE BACTERIA

By definition, fecal-borne bacteria arefrom the small intestines of mammals,and their presence is indicative of thepresence of sewage and other fecalmaterial. However, the bacterial indica-tors cited in this report that are used toassess sewage contamination; total andfecal coliforms, enterococci, E. coli andC. perfringens, may be found in other

animals and are all capable of existingoutside of the small intestine and may befound to occur naturally in the environ-ment. Thus, caution is required wheninterpreting the fecal indicator data inefforts to identify sources of pollution.Ongoing studies by UNH/JEL andNHDES are focused on developing meth-ods (Parveen et al., 1999) to identify spe-cific sources of fecal indicator bacteria.

Prior to the efforts in the late 1980sand early 1990s by New Hampshire to

44

0

100

200

300

400

500

600

1988 1989 1990 1991 1992 1993 1994 1995 1996

Fecal coliform concentrations per 100ml

FIGURE 2.15 Fecal coliform concentrations at seven sites in Little Harbor, Back Channel and Portsmouth harbor: 1988-1996.

45

upgrade all WWTFs in the Seacoast,point sources were the major source ofbacterial contaminants in the Great BayEstuary and coast. More recently, themasking effects of point source pollutionhave been drastically reduced to occa-sional malfunctions or storm event over-loading at WWTFs, and nonpoint sourcepollution is now the major source ofchronic contamination.

A summary of the recent status ofsources of bacterial contaminants inshellfish waters was compiled by NHDES(NHDES, 1995). It lists WWTFs, CSOs,and urban stormwater as the majorsources of bacteria, and unidentifiednonpoint sources as important in someareas. In the following section, the exist-ing information on these and othersources will be described.

2.2.2.1 Storm-related Runoff

The most common source of bacterialcontamination in New Hampshire isrunoff resulting from rainfall/snowmeltevents in urban and urbanizing areas.This conclusion is based on the elevatedconcentrations of bacteria detected in allareas following rainfall events and theproximity of urbanized areas to tidalwater sampling sites, as reported inalmost every recent study. Some refer-ence to stormwater effects in the differ-ent areas have already been cited.

The best illustrations of the impact ofstorm events on surface water quality aresome recent projects conducted by JEL.The first is a three-year study on theeffects of storm events on water qualityin the tributaries of the Great Bay Estu-ary, as summarized in Jones and Langan(1996a). Statistical analysis of the cumu-lative 3-year data showed significantlyhigher bacterial concentrations followingstorm events at every freshwater andestuarine site (Figure 2.6 and 2.7). Thefreshwater sampling sites were all locat-ed at the tidal dams, all of which arelocated within urbanized areas of thenearby municipalities of S. Berwick, MEand Dover, Durham, Newmarket andExeter, NH. More detailed studies of thewatersheds around the Exeter (Jones andLangan, 1995c; NHOSP, 1995a) and the

Oyster (NHCP, 1996; Jones and Langan,1993a; 1994c) rivers have confirmed thaturban runoff is an obvious source ofcontamination in these areas. This issueis presently being addressed by supportfrom the NHEP and other ongoing proj-ects. Some municipalities have invento-ries of stormwater outfalls. Those thathave inventories include Greenland andparts of Dover, Rochester and Seabrook.However, the quantity and quality of theinformation varies, making it difficult toformulate a clear picture of the magni-tude of stormwater outfalls as potentialpollution sources.

A better understanding of contami-nants in stormwater runoff has beenrecently emerging. NHDES (1997) foundsignificant dry weather contamination instormwater pipes draining into theCocheco and Squamscott rivers. A fol-low-up study included wet and dryweather sampling in the Bellamy andCocheco rivers (Landry, 1997). Signifi-cant contamination was observed in theCocheco storm drains during dry weath-er and the Bellamy drains in wet weath-er. More comprehensive studies by Jones(1998) and Jones et al. (1999) focused onthe worst of the drains on the CochecoRiver and showed contaminants flowedfrom the drains continuously during dryand wet weather, in some cases at highconcentrations.

Other recent studies on stormwatercontamination have been designed toassess the effectiveness of stormwatercontrol measures. Jones and Langan(1996b) focused on ten differentstormwater control systems in the NHSeacoast region during 1995-96, includ-ing swales, retention ponds, a pond withstaggered dikes and an infiltration cham-ber. First flush (during the first 0.25 inch-es of rainfall) samples were analyzed fora variety of contaminants, including bac-terial indicators. Results showed that wetponds were more consistently effectiveat treating diverse contaminants thanswales. During summer, bacterial con-centrations increased both in influentand effluent water, and all systems wereless effective at removal. The results sug-gest that bacteria may re-grow in the

moist, nutrient-rich control systems dur-ing dry periods that occur betweenstorms. Elevated concentrations are thendischarged with new storm events. Thisraises the issue of the public health sig-nificance of stormwater runoff. It alsosuggests that some system designs maynot be effective in treating bacterial con-taminants. A follow-up study (Jones,1998c) of five systems during dry weath-er showed evidence of some growthoccurring during summertime in somesystems and suggested certain conditionsmay be conducive to growth.

The 1996 New Hampshire WaterQuality Report to Congress 305(b)(NHDES, 1996b) reported that 17.3square miles of coastal estuaries are notfully supporting uses because ofpathogen indicators, and that the sourceof bacteria is unknown. It states thatstormwater runoff is a well-documentedsource of bacteria and nutrients, citingnumerous studies (Jones and Langan,1996a; 1996b; NHCP, 1996; Swift et al.,1996). Stormwater was also cited as a sig-nificant source in coastal New Hamp-shire in another DES report (NHDES,1995). The 305(b) report also pointed outthat rainfall is a condition for closure ofHampton Harbor because of runoff-asso-ciated bacteria, as reported in the sani-tary survey (NHDHHS, 1994b).

Other studies in New Hampshire haveshown degradation of surface waterquality from rainfall runoff. The runoffwater from seven storm events in twodeveloped areas in Concord had fecalcoliform concentrations ranging from 23to 240,000/100 ml (NHWSPCC, 1979). Amore recent study (Comstock, 1997)found E. coli concentrations in stormwa-ter runoff consistently exceeded statewater quality criteria at both an urbanand a residential site. Water quality inGreat Bay was reported to be degradedduring periods of high rainfall and runoff(NHDHHS, 1992). Several street drainagesystems in Hampton and drainage ditch-es in Seabrook, some of which containedfecal contaminants, were found to draindirectly into the marsh and tidal watersof Hampton Harbor (NHDHHS, 1994).NHDES (1997) also reported stormdrain

catch basins with high E. coli concentra-tions in Hampton.

The most intensive study on stormwa-ter was conducted by the NH Water Sup-ply and Pollution Control Commission(NHWSPCC) in 1983 as part of the EPANationwide Urban Runoff Program (Oak-land, 1983). The impacts and methodsfor control of stormwater were studied intidal and freshwater portions of the Oys-ter River watershed in Durham, NH.Water quality in the watershed declinedsignificantly following storm events,especially for total and fecal coliforms.Because Durham maintains a separatestormwater and sanitary sewer system,sources of contaminants during stormswere suspected to be from animal feces.Sources for dry weather contaminationwere not identified. Studies on stormwa-ter runoff control measures showedfavorable effects on bacterial contamina-tion with parking lot vacuum cleaningand a river-run impoundment (MillPond), but not with a grassed swale. Thegrassed swale showed significantremoval of inorganic nitrogen, butorthophosphate and bacteria concentra-tions increased. The river-run impound-ment, in contrast, showed significantremoval of mass loads for bacteria andinorganic nitrogen, with a non-significantincrease in orthophosphate, with lengthof detention time a positive factor.

The major Best Management Practices(BMPs) used to control urban runoff inNew Hampshire in 1989 were treatmentswales and sedimentation basins(NHDES, 1989a). The report suggestedthat these control measures are effectivefor trapping sediments, controlling ero-sion and removing some heavy metals.However, the report recognized thesesystems as being ineffective at treatingnutrients, bacteria, oil and suspendedsolids. New rules for stormwater controlmeasures for large developments havebeen adopted, and a new manualdescribing acceptable control systemshas been published (NHDES, 1996). Theeffectiveness of each type of system fortreating a range of different contaminantsis presented, along with advantages, dis-advantages and design criteria.

46

47

Stormwater runoff is considered tobe a serious nonpoint source pollutionconcern by 68% of polled residents ofthe Oyster River watershed (Hanratty etal., 1996). Even though 87% said thatproblem storm drains should beupgraded, they were largely unwillingto pay for corrective actions. NHDESestimated that rehabilitation of coastalcollection systems and treatment ofstormwater would cost $100-200 million(NHDES, 1995), and that the chances ofsuccessful treatment of bacterial con-taminants is slim. For ongoing work inthe Seacoast, NHDES considers thisissue a significant problem, and it is amajor focus of the latest NHDES CoastalBasin Nonpoint Source PollutionAssessment and Abatement Plan(NHDES, 1996a). Present efforts byNHDES and UNH/JEL are focused oninvestigating stormwater systems duringdry and wet weather, and following upon problems in tributaries to coastalrivers identified in previous JEL, NHOSP,NHDHHS and NHDES studies.

Unlike previous studies that oftenconclude that animal feces is the majorsource of microbial contaminants instormwater runoff from urban areas, themajor source of contaminants in NewHampshire coastal urban runoff appearsto be direct sewage contamination fromleaking pipes and illicit connections.Thus, even though there may be sepa-rate sewage and storm drain systems,their age, design and close proximitybelow the surface appear to be con-ducive to cross contamination.

2.2.2.2 Wastewater Treatment Facilities and Combined Sewer Overflows

WWTFs are, ideally, capable of reducingmicrobial contaminant concentrations tomeet required criteria in wastewater100% of the time. However, this does notoccur in practice. Changes in wastestream characteristics that modify treat-ment efficiency, equipment problems,operational changes, human error andacts of God (hurricanes, lightning,storms) all influence the effectiveness ofWWTFs. The WWTFs in New Hampshire

and their effluent flow ranges are pre-sented in Figure 2.16. NHDES recordsthe number of upsets that facilitiesreport, although documented impacts ofupsets in treatment processes on surfacewater quality are rare (Jones and Langan,1993a; 1994c). Reporting of upsets hasincreased in recent years resulting in bet-ter characterization of the problem(NHDES, unpublished data). WWTFsreport upsets to NHDHHS so shellfishareas can be closed. All coastal WWTFshave a limit of 70 total coliforms/100 mlat discharge pipes, they are required toconduct daily testing and chlorine resid-uals are required to be low/non-toxic. Afew WWTFs still have problems meetingthe total coliform discharge limit, andmodifications to disinfection systems arebeing planned for most of these systems.

Some coastal WWTFs and sewer sys-tems have limited capacities for handlingstormwater during major storm events.Stormwater can overburden facilities andrequire bypassing of pump stations.Under these conditions, inadequatelytreated wastewater is discharged to tidalwaters and significant loading of bacteriacan occur. This happens several timeseach year and shellfish beds downstreamfrom the affected facilities have beenclosed. The ‘100 year’ storm of October,1996 caused bypasses in all but a fewcoastal WWTFs. Other stormwater relat-ed problems include infiltration ofstormwater and high groundwater intosewer pipes. This may result in leakageof pipes. It is suspected to be a problemin all urban areas, and has been docu-mented in Durham (Jones and Langan,1994c). The problems and the extensivedocumentation of high levels of contam-ination in tidal waters following majorstorm events are the basis for closing thewhole coastal area to shellfishing untilwater quality returns to acceptable levelsand shellfish have depurated contami-nants. The state has made manyimprovements in WWTFs throughout thecoastal area (Table 2.4), and these effortscontinue (NHDES, 1996d).

The two remaining CSOs inPortsmouth are significant sources ofbacteria that impact the water quality of

48

FIGURE 2.16

Municipal wastewatertreatment facilities. Municipal Wastewater

Treatment Facility (WWTF)

FarmingtonWWTF

MiltonWWTF

RochesterWWTF Somersworth

WWTFBerwick, MEWWTF

RollinsfordWWTF

South Berwick, MEWWTF

DoverWWTF

Newington WWTF

Kittery WWTF

PortsmouthWWTF

SeabrookWWTF Seabrook

WWTF(outfall)

Hampton WWTF

NewmarketWWTF

EppingWWTF

NewfieldsWWTF

Exeter WWTF

DurhamWWTF

49

Little and Portsmouth harbors.Portsmouth has eliminated eight of tenCSOs, but two remain in South MillPond. A concern for the Little Harborarea is that contaminants flushed intoSouth Mill Pond from the CSOs couldflow through the Back Channel area intoLittle Harbor (NHDES, 1995). Eliminationof the remaining CSOs would cost anestimated $10 million, as estimated bythe city’s CSO Facility Plan. Because ofthe high costs associated with elimina-tion of the CSOs, the City of Portsmouth

has filed for a Use Attainability (UAA)Study to reclassify the receiving waters,i.e., South Mill Pond. If they are success-ful in proving that the costs are essen-tially prohibitive, then they would not berequired to attain the limit of 70 total col-iforms per 100 ml in South Mill Pond. Insuch a case, careful attention to thepotential for storm-related contaminationto affect any opened shellfish beds in Lit-tle Harbor would be necessary. It wouldalso be difficult to open the extensivemudflats in the Back Channel area.

Wastewater flow (mgd) DateCity design ave.* max.* Control measure completed Cost

Dover 4.4 new 2° treatment facility 1991 $24,300,000

Strafford Co. Facility cease discharge to Cocheco R. 1992

Durham 2.5 1.0 4.5 upgrade from 1° to 2° treatment 1981equipment upgrades 1992-93dechlorination 1995

Exeter 3.0 1.6 6.2 lagoon system built; dechlorination 1990 $5,900,000all but one CSO disconnected 1992 $3,400,000

Farmington 0.4 secondary clarifier 1994-95

Hampton 3.5 sewer project and dechlorination 1993 $4,400,000

Newfields 0.1 0.04 0.2 construction of facility 1983

Newmarket 0.9 0.6 2.5 upgrade from 1° to 2° treatment 1986 $1,900,000dechlorination/dewatering system 1993

Newington 0.3 upgrade disinfection system 1995 ~$350,000

Portsmouth 7.0 new advanced 1° treatment & dechlorination 1992 $15,000,000eliminate 10 CSOs 1991 $5,800,000

Rochester 3.9 currently designing new advanced treatment

Rye sewers connected to Hampton POTW 1991 $2,400,000Wallis Sands St. Pk. UV disinfection; refurbish sand filter 1993

Seabrook construction of wastewater treatment facility 1995

Somersworth 2.4 various improvements; P reduction study

Star Island construction of seasonal 2° treatment plant 1994-95

* in 1994

Point source pollution control program activities from 1988-1996: WWTFs and CSOs. TABLE 2.4

Ongoing work is focusing on ahydraulics study of the CSOs aroundSouth Mill Pond, identification and elim-ination of illicit connections and dyestudies of the WWTF outfall pipe. A safe-ty zone around the outfall pipe will prob-ably extend into the nearby BackChannel.

One CSO remains in Exeter. The CSOis a source of bacteria during stormevents when the capacity of the mainpump station is exceeded. Under thoseconditions, sewage can overflow intoClemson Pond, which acts as an emer-gency holding pond. However, the waterthat drains from the pond to the Squam-scott River is often contaminated(NHOSP, 1995; Jones, 1990).The problemis currently under investigation. Exeterpassed a warrant article in 1999 to allo-cate $1.7 million to address the CSOproblem.

As previously stated, the system ofwastewater treatment facility pipes thattransport sewage from sources to thetreatment plant are a potentially signifi-cant source. In several coastal NewHampshire municipalities, downtownstormwater drains have high concentra-tions of fecal contaminants, even duringdry weather (NHDES, 1997; NHDES,1998; Jones, 1998b). This suggests thatsewer pipes that cross paths with thestorm drains may leak contaminants intothe drains. During runoff events, con-taminants that accumulate in the drainsare washed into the receiving waters.Thus, the system of pipes associated withmunicipal sewage treatment facilitiesmay be sources of contaminants. Theestimated cost for rehabilitating thesesystems in the coastal urban areas is wellin excess of $200 million (NHDES, 1997).

2.2.2.3 Septic Systems

Many shoreline areas adjacent to theshellfish waters of New Hampshire arestill served by septic systems. These sys-tems contain high levels of bacteria andnutrients (Jones, 1998d) that can leachinto groundwater. An extensive two-yearstudy in Seabrook focused on the poten-tial for existing, operational residentialseptic systems to contaminate groundwa-

ter and adjacent surface waters (Jones etal., 1996; 1995). Little evidence of sig-nificant contamination of groundwaterdowngradient from septic systems couldbe documented. At one site with a highwater table, bacterial contaminants weredetected ~9 meters downgradient in thegroundwater. Analysis of saturated soilcores showed the presence of high con-centrations (>100,000/g soil) of C. per-fringens, evidence of long-term andprobably cumulative contamination.Other sites also had contaminated soilsat downgradient (away from the systemin the direction of groundwater flow)areas. The main limitation of any studyof subsurface environments is the diffi-culty of finding contaminant plumeswithout extensive exploration. Thestudies concluded that septic systemsare indeed potential sources of contam-ination to tidal waters when systems arelocated close to the shore, especially indensely populated areas in soils withhigh water tables and course-grained,excessively-drained soils.

Seabrook has recently connected allresidences and businesses to their newsewer system. There are still housesclose to tidal waters that remain on sep-tic systems in Hampton and HamptonFalls (NHDHHS, 1994a). The impact ofdisconnecting the septic systems onwater quality was investigated by Jones(1997). No significant improvement inHarbor water quality was observed,possibly because the Mill Creek areahad not yet been connected to theWWTF.

Septic systems are numerous aroundthe Little Harbor area in Rye and insome areas in New Castle (Jones andLangan, 1996c). Septic systems are alsocommon around Great and Little bays(Jones and Langan, 1995b), the Squam-scott River (Jones and Langan, 1995c)and in the Oyster River watershed(Jones and Langan, 1994c; 1993a). Largeareas with houses served by septic sys-tems are also present along the coastand the Piscataqua/Cocheco/SalmonFalls River areas. Thus, septic systemsare a widespread, documented potentialsource of contamination.

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2.2.2.4 Agricultural Runoff and Other Nonpoint Sources

On a statewide basis, agriculture has notbeen a significant nonpoint source prob-lem (NHDES, 1989a). The number offarms in New Hampshire and StraffordCounty have been declining over thepast 25 years. However, horse farms areincreasing. Certain activities have beenproblems on local levels, includingmanure storage and spreading practices,stable management and milk housewaste management. Rockingham CountyConservation District has information oncontaminant runoff and managementstrategies for mitigating specific farmsites in the county. UNH/JEL and NHDESconducted studies at a farm in Strathamto determine the effectiveness of con-structed wetlands on microbial and nutri-ent contaminants (Jones and Langan,1992; 1993b). The construction of a wet-land within the drainage swale betweenthe manure storage area and the Squam-scott River had no beneficial effects oncontaminants during the first year afterconstruction (Jones and Langan, 1993b).Concentrations of fecal indicator bacteria(fecal coliforms, enterococci, E. coli andC. perfringens ) were all detected at ele-vated concentrations (> 105/100 ml) justbelow the manure pile, and at lowerconcentrations downstream. A similartrend was observed for nutrients (ammo-nium, nitrate/nitrite, orthophosphate).

Agricultural use of land within mostgrowing areas have been documented(NHDHHS, 1994a; 1995; Jones and Lan-gan, 1996c). Many of the cited farms arepracticing responsible management pro-cedures to prevent animal waste fromcontaminating bordering water bodies.

There are other potential sources ofbacterial contamination near and withinNew Hampshire’s shellfish waters,including storm and parking lot drains,snow dump sites, boats, wildlife andresuspended sediments. A guide forBMPs to control most potential nonpointsources of pollution is published(NHDES, 1994c) and serves as a usefulreference. NHDES has recently been suc-cessful in improving and increasing thenumber of coastal boat pump-out facili-

ties. Further improvements are expectedeach year. Recent sanitary surveys forsome coastal waters include marinaassessments (NHDHHS, 1994; 1995;Jones and Langan, 1995b; 1996c).

Animal feces is often mentioned as aprobable source of bacterial contamina-tion in stormwater runoff (Jones, 1999;Oakland, 1983). In almost every case, thejustification for such conclusions is thatno human source could be identified, sothe investigators conclude that animalwaste must be the source, usually with-out any direct documentation. Recentstudies have shown many previouslyunsuspected sources of stormwater con-tamination exist in coastal New Hamp-shire towns, including stormwater drains,sewer pipes, stormwater treatment sys-tems, etc., including areas where animalfeces had been previously suspected(Jones and Langan, 1996b; Jones andLangan, 1993a). More recent studies haveshown underground sewage pipes con-taminate stormwater drains in urbanareas (Landry, 1997; Jones, 1998b). It islikely that human sources of fecal con-taminants remain more significant thananimal sources in New Hampshire’s Sea-coast (Jones, 1999). However, the issueof the source of nonpoint source pollu-tion, whether it is of human, animal orother origin, is an extremely importantquestion to address. Not only is it neces-sary for identifying the source of con-tamination, but it is essential fordetermining the public health signifi-cance of fecal contamination. A newstudy by NHDES and UNH/JEL will usenew biotechnological methods to differ-entiate between human and othersources of E. coli isolates from NewHampshire coastal waters.

Rye Harbor

2.2.3 MODELING AND DYE STUDIES FOR BACTERIAL FATE ANDTRANSPORT

Computer modeling of stormwater runoffimpacts to the tidal portion of the OysterRiver was conducted as part of a studyby Oakland (1983). The goal was toassess impacts relative to state standardsfor coliform bacteria and dissolved oxy-gen standards, and assess effectivenessof stormwater control measure imple-mentation. The results of the modelingconfirmed observations that coliformstandards would be violated routinelyduring storm events. Violations, evenduring dry weather, would be most fre-quent at upstream sites and during ebbtides. Dissolved oxygen standardswould be violated much less frequently,only during 28% of storms. The viola-tions would be expected to be short-lived during ebb tides only in the upperreaches of the tidal river. The modelfound that only Mill Pond, as a river-runimpoundment, would have significantimpacts on coliform loading, while vac-uum cleaning of impervious surfacescould significantly reduce BOD loading.

Numerous dye studies have beenconducted to determine potential con-tamination plumes and contaminanttransport from various point sources.Ballestero (1988) reported on a field dyestudy and calculations for dilution anddispersion using MERGE, a contaminantplume modeling program, for the newDover wastewater treatment plant out-fall diffuser in the Piscataqua River. Thepurpose of the study was to determinewater quality criteria for conservativecontaminants in the effluent. The zoneof initial dilution was set by the state tobe 0.25 miles upstream and downstreamfrom the diffuser. Average dilution atthese distances was calculated to be26,000, with significant dilution occur-ring as a result of the initial jet aspira-tion from the diffuser as the effluententered the river. A modeling study wasalso conducted for a proposed diffuserfor the Newmarket WWTF.

Other dye studies have been con-ducted to establish safety zones for

shellfish harvesting around WWTFs andmarinas. A recent dye study was con-ducted by the US EPA at the Great BayMarina in Little Bay, but the results havenot yet been published. In HamptonHarbor, a dye study was conducted todetermine the safety zone downstreamfrom the Hampton WWTF (Fugro-McClelland, 1993).

In Great Bay, the most recent sanitarysurvey (NHDHHS, 1995) identified theWWTFs in Durham and Newmarket asthe plants with the greatest chances ofimpacting shellfish harvesting. Therehave been recent dye studies conductedat both sites, but the data are not yetpublished. An EPA model, CORMIX,was used to model discharges of fecalcoliforms from the WWTFs (Langan andJones, 1995a). At the NewmarketWWTF, the worst case scenario was fora release at mid-falling tide, in whichcase the plume would reach the mouthof the Lamprey River in 7.2 h with aconcentration of 750 fecal coliforms/100ml. The mouth of the river is an areaclassified as prohibited for shellfish har-vesting. Thus, another model (Brownand Arrelano, 1979) was used to esti-mate time for the plume to reach theclosest approved areas. It was estimatedthat the total time for the plumereleased at mid-falling tide to reachrestricted waters is 28 h, which is suffi-cient for closing the area to shellfishing.At the Durham WWTF, the worst casescenario was found to be a release athigh tide, in which case the plumewould reach the mouth of the OysterRiver in 4.2 h with a concentration of420 fecal coliforms/100 ml. Furthertransport of bacteria to the LangleyIsland area could take a total time froma high tide release of 8-12 h.

In Hampton Harbor, CORMIX wasused to model transport and survival ofbacteria discharged from boats mooredin Seabrook Harbor during fall-springwhen the clam flats in the Harbor areopen for harvesting (Langan and Jones,1995b). Model simulations were run forboth a slug release and a slow, continu-ous release of bacteria over a six hourtime period from the vessels. The con-

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centrations of bacteria in the plume atthe edge of the adjacent clamflat forboth types of releases were 13 and 0.02fecal coliform/100 ml, respectively,which are both below the regulatorylimit of 14 fecal coliforms/100 ml. Theconclusion of the study was that theboats present during colder months donot pose a risk of significant contamina-tion to adjacent clamflats. However,because boating activity increases signifi-cantly during warm months (mid-May tomid-September) it is recommended thatclamflats remain closed during thesetimes. This study did not address theHampton Marina, which typically hasmany more boats than Seabrook Harbor.

Current direction and velocity meas-urements have been used to help pre-dict bacterial transport and impact toshellfishing areas in Hampton Harbor(Langan and Jones, 1995b) and LittleHarbor (Jones and Langan, 1996c). InLittle Harbor, transport of bacteria dis-charged from boats at the WentworthMarina and in the nearby mooring areato shellfishing areas were modeledusing estimated discharges and currentvelocities and directions. Using a varietyof scenarios, the modeling effort foundit likely that water with fecal coliformconcentrations exceeding 14/100 mlcould reach clamflats under worst caseconditions. Jones and Langan (1996c)recommended that shellfishing beallowed only during colder monthswhen boat traffic and usage is negligi-ble.

2.2.4 IMPACTS OF FECAL-BORNE BACTERIA ON SHELLFISHING

New Hampshire has abundant and valu-able shellfish resources. Many citizenshave enjoyed the recreational harvest ofclams, oysters and mussels over the yearsin Great and Little bays, Hampton Har-bor, Rye Harbor and Little Harbor. How-ever, during the past few decades, all orportions of these areas have been closedfor shellfishing because of unacceptableconcentrations of bacterial contaminants.Much effort has been dedicated to deter-mining which areas are safe for shellfishharvesting and how to open other areas.

2.2.4.1 Historic Sanitary Assessments of Shellfish-growing Waters

Bacterial contamination of the shellfishgrowing waters of New Hampshire hasbeen a challenging, continuous problem.New Hampshire has assessed the sani-tary conditions of tidal water bodiessince 1957 (NHWPC, 1960). Early data onbacterial contamination Jackson (1944)reflected the high loading of untreatedsewage into the tributaries to Great BayEstuary: every tributary had average totalcoliform concentrations of >800 /100 ml.Total coliform concentrations were muchlower at sites in Great and Little bays,although still elevated compared to morerecent data and in excess of the limit of70 total coliforms/100 ml for shellfishing.

Early routine state assessments of thesanitary quality of tidal waters began in1957 (NHWPC, 1960). The 1960 reportincluded a map delineating suitability ofwater quality for shellfishing in the Pis-cataqua River/Great Bay Estuary (Figure2.17). Only a small portion of easternGreat Bay (Greenland Bay) near theshore between Fabyan and Piercepoints was classified as suitable foryear-round harvest of shellfish for directmarketing. The rest of the estuary wasconsidered unsuitable for year-roundharvesting because of the continuouspresence of pollution by raw sewage,except for much of the central area ofGreat Bay and the outer deeper areas ofPortsmouth Harbor. The classificationwas based on only a few samples (onesample/site in some cases). By 1975,New Hampshire published shellfishwaters classification maps based on amedian 70 total coliform/100 ml limit forClass A tidal waters (Figures 2.17 and2.18; NHWSPCC, 1975). Areas wheremedian total coliform concentrationswere <70/100 ml included eastern GreatBay between Nannie Island and BirchPt. beyond the mouth of the WinnicutRiver, two areas near the western shore-line around the Footman and VolsIslands, the lower tidal portions of theOyster and Bellamy rivers, Little Harborand southern portions of the BackChannel, outer Portsmouth Harbor, thenorthern half of Hampton Harbor and

54

FIGURE 2.17 Great Bay Estuary shellfish waters classification trends from 1960 to 1998.

Areas open to the publicSuitable for year-round harvest

Not suitable due to probable pollution

Not suitable due to continuous pollution

Approved

Conditionally Approved

Restricted

Prohibited

Prohibited/Safety Zone

Unclassified (closed)

Approved

Conditionally Approved

Restricted

Prohibited

Prohibited/Safety Zone

Unclassified (closed)

1960 1975

1990 1998

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Approved

Conditionally Approved

Restricted

Prohibited

Prohibited/Safety Zone

Unclassified (closed)

Approved

Conditionally Approved

Restricted

Prohibited

Prohibited/Safety Zone

Unclassified (closed)

Approved

Conditionally Approved

Restricted

Prohibited

Prohibited/Safety Zone

Unclassified (closed)

1975

1990 1998

Hampton Harbor Estuary shellfish waters classification trends from 1975 to 1998. FIGURE 2.18

lower portions of some tributaries, RyeHarbor and the whole of New Hamp-shire’s Atlantic coast. Point sources,especially the WWTFs, were the majorsources of contamination, and upgradesand construction were slated to occurwithin a few years of the reports for allareas not currently treating waste withthe best available technology.

Contaminated shellfish waters becamean even more important issue for thepublic and their legislative representa-tives after the NHDHHS closure ofHampton and Little harbors in March,1989 (NHDES, 1989a). A Shellfish Com-mittee was formed in March, 1988, andensuing efforts focused on identifyingsources of contaminants and eliminatingthem where possible. A report was writ-ten by the agency personnel on the com-mittee in 1989 entitled “InteragencyReport on the Shellfish Waters of NewHampshire” to outline what steps wereneeded to reopen shellfish beds. Thereport included a few, high priority rec-ommendations/actions:

■ prioritize the elimination of sourcesof bacterial contaminants and con-duct a cost/benefit analysis relatingremediation costs to the value ofshellfish harvest activities;

■ increase the effectiveness and efficiency of existing WWTF wastewater disinfection systems;

■ communities should survey shore-lines and eliminate nonpointsources of pollution;

■ identify sources of pollution whereobvious point sources are present;

■ prioritize state and federal funding to support WWTF construction and nonpoint programs in coastalcommunities.

The State began to make progress oneach of the key recommendations soonafter the 1989 Interagency Shellfish(Flanders, 1989) report was published.By 1991, improvements had been madeto Dover, Exeter, Newmarket, Hamptonand Portsmouth WWTFs (NHF&G,1991). Some failed septic systems were

identified and abated in Seabrook, Ryeeliminated its coastal discharge of rawsewage by building a sewer line toHampton and all but two CSOs wereeliminated in Portsmouth. Shoreline sur-veys were conducted in Great Bay andthe Bellamy River by state agencies (seebelow), while sources of contaminationin the Bellamy River were identified andabated. Some remote residential areas inHampton were connected into the townsewer system. For all growing areas(Great/Little Bay; Little Harbor; Hamp-ton Harbor; Rye Harbor), specific waterquality problem areas were identified,described and prioritized. Concurrentwith these efforts were a number ofwater quality monitoring programs runby state agencies and UNH. The shell-fish program continued monitoringwaters to support classifications,NHDES continued monitoring someupstream areas as part of their ambientwater quality monitoring program, andUNH/JEL initiated monitoring in GreatBay as part of the GBNERR program.However, the 1991 report (NHF&G,1991) recognized the need for moreextensive water quality monitoring inkey areas to document improvements inwater quality and to support reclassifi-cation of areas. The improvements inWWTFs and elimination of major pointsources of contamination also providedconditions conducive to assessing NPSpollution.

The shellfish growing waters of GreatBay were the focus of shoreline/sanitarysurveys in 1988-91: the Bellamy River(NHDES, 1991) and Great Bay (NHD-HHS, 1992). The Bellamy River surveyfound an unpermitted pipe dischargingbacterial contaminants near the Sawyer’sMill apartments in Dover near the tidaldam. No evidence of failed septic sys-tems or other nonpoint sources of con-tamination was detected, and furtherstudies were recommended. In the GreatBay sanitary survey, water samples col-lected along the northwest shoreline ofGreat Bay were all elevated (330-3,300total coliforms/100 ml) above the totalcoliform limit of 70/100 ml (NHDPHS,1992). The dominant source of contami-

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nation was considered to be WWTFs dis-charging into nearby tributaries.

Indigenous estuarine bacterialpathogens like vibrios have been a sig-nificant public health concern in thesouthern areas of the US. In NewHampshire, there has been no docu-mented evidence of food poisoning orwound infections in the local communi-ties associated with the incidence of anyVibrio sp., except for an incident of V.parahaemolyticus gastroenteritis result-ing from consumption of oysters takenfrom Great Bay waters that occurred inJune, 1992 (Dr. R. Rubin, personal com-munication).

2.2.4.2 Present Conditions

A recent sanitary survey in Great Baywas conducted (NHDPHS, 1995; Jonesand Langan, 1995b). The approved areawas expanded northward in Little Bayfrom the cable crossing (Figure 1-6)based on monitoring at NHDHHS sta-tions (Figure 2-3). The northern bound-ary for the approved area now extendsfrom Fox Point (43°07’10” N. Latitude,70°51’35” W. Longitude) to the westernshore of Little Bay at Durham Point(43°07’14” N. Latitude, 70°52’10” W. Lon-gitude). A new sanitary survey and relat-ed studies have focused more intensivemonitoring in lower Little Bay and theBellamy River (NHDHHS, 1998; Jones,1998a). The shoreline survey and fecalcoliform concentrations at five of the sixsites were consistent with an approvedclassification of much of lower Little Bay.Initially, only an area around Broad Covewas classified as approved, as otherareas required additional samples. In1998, most of the rest of lower Little Baywas re-classified as approved, except foran area from the mouth of the OysterRiver east to Fox Point, and areas aroundthe two marinas. In Great Bay, a restrict-ed area has been established in thesouthwestern corner of Great Baytoward the mouths of the Lamprey andSquamscott rivers. The classification ofeastern Great Bay has been clarified andis almost all approved, except GreenlandBay south of a line extending from PiercePoint west to the Greenland shoreline.

Little Harbor was the focus of a pre-liminary sanitary survey in 1995-96(Jones and Langan, 1996c). Water qualitywas found to meet approved classifica-tion standards in Little Harbor, and nosignificant sources of pollution were doc-umented. The Wentworth Marina wasconsidered to be a significant potentialsource of bacterial contaminants. Apumpout facility replaced in 1997 usingClean Vessel Act support and privatefunds. Even though it has pump-outfacilities that are extensively used, suchlarge marinas are regarded as potentiallysignificant sources of contamination rela-tive to classifying shellfish areas. Thestatewide closure of shellfishing duringwarm months, June through early Sep-tember (November for Hampton Har-bor), coincides with the timing of thegreatest use of the marina, mid-Maythrough mid-September. The absence ofboaters at the marina during coldermonths resulted in little impact of themarina on water quality (Jones and Lan-gan, 1996c), and would probably not bea concern if the area was opened duringcold months for shellfishing.

In the rest of the Little Harbor area,the Witch and Seavey Creek area hassome problems with water quality andfurther studies are needed to identifysources. The Back Channel area shouldalso remain closed because of the CSOsin Portsmouth and other recently identi-fied sources.

A sanitary survey was conducted inHampton Harbor during 1993-94 to sup-port reclassification of the closed shell-fish waters (NHDHHS, 1994). The studyinvolved intensive water quality monitor-ing, experiments designed to test a vari-ety of conditions and consideration of allpotential and known pollution sources.The effort resulted in reclassification ofportions of Hampton Harbor to “condi-tionally approved”, limited by rainfallevents and closed during warm months(June-October) because of the increasedsummer population. The classificationwas based on sampling at NHDHHS sites(Figure 2.12). Elevated concentrations offecal coliforms at a few sites in the har-bor near the mouth of Mill Creek and

near River St. and Cross Beach Rd. wereinvestigated further in 1995 (Langan andJones, 1995a & b). The study and anewer study (Jones, 1997) suggested thatelevated bacterial concentrations mayoriginate from Mill Creek or possiblyfrom resuspended sediments; no clearlydefined sources were found. Improvedwater quality in recent years has resultedin a recent upgrading of the shellfish har-vest classification of the large MiddleGround clam flat in Seabrook fromrestricted to conditionally approved(NHDHHS,1998). Clamming can occurfrom November to May except after rainevents of >0.1 inches of rain in 24 hours.In addition, the rainfall condition ofapproved classification has been modi-fied to be seasonal, with less restrictiveconditions (0.25” rain per 24 h) in effectfor all areas during December throughMarch. It is hoped that complete discon-nection of all septic systems in the areawill result in improved water quality soeven more clam flats can be opened.

2.2.5 MICROBIAL CONTAMINATIONImpacts on Swimming and Other Recreational Uses

There have been no reported incidencesof water-borne disease in New Hamp-shire at least since 1992 (NHDES, 1994a;1996b). Microbial contaminants wouldbe a concern at bathing beaches if swim-mers ingested water and became ill. Bac-terial indicator standards are based onUSEPA studies of disease incidence inassociation with swimming. Thus, theenterococci standard for tidal recreation-al waters was developed to protecthumans from fecal-borne pathogens.The data from the NHDES 305(b) reportsshowed swimming was only restricted atopen ocean sites in 1991-1994 and at acoastal shoreline site from 1988 to 1990.

Some temporary closures of beachesin New Hampshire occur during warmmonths when beaches become over-crowded. The heavy population ofswimmers can cause concentrations offecal-borne bacteria to be present at lev-els that exceed standards, and time isneeded for the water to become cleanagain prior to re-opening beaches.

2.2.6 FECAL-BORNE PATHOGENS Historical Studies on Indicatorsand Pathogens

Historically, there has been a great dealof research in Great Bay conducted byresearchers at the Jackson Estuarine Lab-oratory and the Department of Microbi-ology at the University of NewHampshire on the various aspects ofmicrobial pathogens. The estuary hasserved as a useful site to conduct thesestudies, as sewage discharges have con-taminated shellfish-growing areas for along time (NHWPC, 1960; NHWSPCC,1975; 1981). Slanetz et al. (1964) foundgood correlations between membranefiltration and multiple tube fermentationtests for coliforms in shellfish and water,and showed that not all positive fecalcoliform tubes contained Escherichiacoli. Fecal streptococci and fecal col-iforms were useful indicators of fecalpathogen contamination, as Salmonellasp., and on two occasions, Coxsackieviruses were detected in shellfish andwaters from areas having high levels offecal indicator bacteria (Slanetz et al.,1968). However, Salmonella sp. (Slanetzet al., 1968) and enteric viruses (Metcalfet al., 1973; Metcalf, 1975) were alsodetected in samples of water and oystersfrom areas that met the coliform standardfor approved shellfish-growing waters.One general conclusion of the historicalstudies was that enteric viruses and Sal-monella sp. had a greater ability to sur-vive than indicator bacteria in estuarineenvironments, and that these pathogenswere often associated with irregularintroductions, or pulses, of contamina-tion into the estuary. The findings pro-vided early evidence that contributed togrowing doubts about the adequacy ofusing total coliforms for classifyingapproved shellfish waters, especiallywith low indicator levels. The occurrenceof the specific pathogens Salmonella sp.and enteric viruses was never correlatedwith any reported incidence of diseasecaused by these microorganisms in sur-rounding communities.

The sources and fate of microbialcontaminants in Great Bay were the

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subject of further studies. Metcalf andStiles (1968) found that enteric viruseswere discharged from sewage effluentpipes and disseminated throughout theestuary. The viruses were rapidly takenup by oysters and retained for monthswithin shellfish, especially during coldwinter months. Introduction of chlorina-tion as treatment of sewage by a munic-ipal facility caused dramatic decreasesin coliform, Salmonella, and entericvirus levels, although the pathogenscould still be detected in treated effluenton occasion. Slanetz et al. (1972) foundrapid die-off of indicator bacteria in oxi-dation ponds at three wastewater treat-ment facilities in the estuarine system,especially when three to four ponds insuccession were used to treat waste-water. However, Salmonella and entericviruses could be isolated from all ponds,especially in cold (1-10°C) water. Suchfindings are important relative to theoyster harvest season in Great Bay,which spans the cold autumn throughspring months and is only closed duringthe warm summer months. More recentstudies on pathogens in oysters fromthe Piscataqua River showed nodetectable Salmonella sp. in shellfishprior to processing at a commercialshellfish depuration facility in Maine(Jones et al., 1991).

Presently accepted methods fordetecting enteric viruses are too expen-sive, slow, and complex to be adoptedfor routine analysis of water and shell-fish. However, more rapid and precisemethods for detecting enteric viruses arebeing developed at UNH. For example,application of radioactively labeledcDNA probes for poliovirus and Hepati-tis A virus showed the presence of theseviruses in shellfish and water fromclosed areas in Great Bay (Moore andMargolin, 1993; Margolin and Jones,1990; Margolin et al., 1990). Gene probeassays showed good agreement with tra-ditional tissue culture methods for virusdetection. Comparison of virus inci-dence with levels of bacterial indicators

in the Oyster River revealed no cleartrends. Levels of bacterial indicatorswere consistent with the classification ofthe river as prohibited for shellfishing,but showed little relationship to thepresence or absence of enteric viruses.

An ongoing study is focusing on viralcontamination of groundwater in north-ern New England (D. Heath, personalcommunication). Total culturableenteric viruses and PCR analysis ofpoliovirus, hepatitis A and Norwalkvirus are being measured in comparisonto other microbial indicators and dis-solved nutrients. Groundwater samplesare being collected from drinking waterwells located in close proximity to sep-tic systems and that have had past con-tamination problems.

Water quality sampling

A.

REID

2.2.7 AUTOCHTHONOUS MICROBIAL PATHOGENS

Non-fecal bacterial pathogens that areindigenous to and common inhabitants ofestuarine environments are also potentialhealth hazards. In particular, the Vibri-onaceae have been associated with shell-fish-borne disease incidence and woundinfections resulting from exposure tomarine waters (Rippey, 1994). Bartleyand Slanetz (1971) found Vibrio para-haemolyticus in oysters and estuarinewater from Great and Little bays in Sep-tember and at decreasing levels throughNovember. V. parahaemolyticus has alsobeen detected in oysters (Jones et al.,1991) and water (Jones and Summer-Bra-son, 1998; Summer-Brason, 1998; Jones etal., 1997) from the Estuary in more recentstudies. Another vibrio, V. vulnificus, wasdetected in 1989 for the first time north ofBoston Harbor in the Maine and NewHampshire waters of the Great Bay Estu-ary (O’Neill et al., 1990). This discoverydid not necessarily mean that it was a

new inhabitant of the estuary. Many otherreasons are related to why it had notbeen previously detected, including noone had tried to detect it, it was only rec-ognized as a bacterial species in the late1970s and there was no incidence of V.vulnificus-related disease to cause alarm.It has since been detected routinely in allof the tidal portions of the major tributaryrivers of the estuary, where shellfishing isnot permitted, but detection is extremelyrare and at low concentrations in theareas of Great Bay open to shellfishing(Figure 2.19; Jones et al., 1997; O’Neill etal., 1990; Jones et al., 1991). A relativelyhigh incidence of hemolysin-negative, orpotentially non-virulent strains of V. vul-nificus have been isolated from the estu-ary (O’Neill et al., 1991).

More recent studies in Great Bay andthe Oyster River helped to delineate theecology of V. vulnificus. This is impor-tant for prediction of conditions that mayresult in higher concentrations of theorganism and for developing post-har-vest processing strategies for eliminating

60

Squamscott R.Chapmans

Landing

Squamscott R.and Lamprey R.

mouths

Great Baycenter

Adams Point Oyster Rivermouth

Oyster RiverWWTF outfall

Oyster Rivertown landing

611

288

89 111 104

755

822

381

187

71 7094

397

784

V. parahaemolyticusV. vulnificus

MPN/100 ml

FIGURE 2.19 Geometric mean Vibrio vulnificus and Vibrio parahaemolyticus concentrations at low tide (MPN/100 ml) in Great Bay Estuary by site during June-September, 1993-95.

Numerous historical and currentstudies have focused on organic

contaminants, metals and metalloids incoastal New Hampshire, especially inGreat Bay. The major sources of infor-mation can be found in reports from the1991-93 ecological risk assessments forthe Portsmouth Naval Shipyard, theGulfwatch 1991-98 annual reports, theArmy Corps of Engineers dredge projectdata, NPDES monitoring data, numerousreports by Normandeau Associates,reports from the former Pease AFB, andscientific papers from a few UNH labo-ratories in the departments of Chem-istry, Earth Sciences and Microbiology.Numerous other studies conducted byprivate firms, the University, and bothstate and federal agencies also provideimportant information. Contaminantsthat have the most available informationinclude chromium, mercury, tin andlead, based on their local distribution,historical and current sources, potentialtoxicity and scientific interest.

Small scale, light manufacturing ispracticed in Portsmouth along the Pis-cataqua River and in many of themunicipalities bordering the Great Bayand Hampton/Seabrook estuaries.There are no industrial activities on theshores of some coastal areas, such asLittle Harbor. Other areas like thePortsmouth Naval Shipyard and PeaseAFB have been the sites of significanthistorical storage and use of toxic con-taminants. An environmental assess-ment of the shipyard and surroundingestuarine habitats has shown elevatedlevels of some toxic compounds indepositional areas and some biota(NCCOSC, 1997). Little evidence of actu-al toxic effects on biota was apparent.The urban areas in the coastal regionhave had a variety of industrial activitiesthat have contributed unknown quanti-ties of contaminants to surface watersover the last three centuries.

Studies have been conducted to deter-mine the concentrations of contaminantsin sediments, in organisms and in the

water column, with some focusing ontheir effects on organisms. Informationon the status and trends of toxic contam-inants in these environmental compart-ments is presented below.

2.3.1 STATUS AND TRENDS FORCONTAMINANTS IN WATER

Lyons et al. (1976) studied trace metaldischarges into the Great Bay Estuary inthe mid-1970s. Measurements were madeof dissolved and “environmentally avail-able” Fe, Mn, Cu, and Cr. Only Cr waspresent at levels in excess of the rangefound for other northern New Englandriver systems. The data indicated a reduc-tion of inputs to the estuary from indus-try compared with what had occurred inthe previous decade. Scattered smallprojects involving analysis of tidal watershave also occurred. For example, waterfrom the Taylor River in the Hampton/Seabrook Estuary was analyzed for ninemetals and ten organic contaminants dur-ing 1985 (ESI, unpublished data). Nelson(1986) reported the analysis of waterfrom four areas in the Great Bay Estuaryfor lead concentrations, which rangedfrom <0.05 to 0.14 mg/l.

More recent studies on contaminantconcentrations in water have been con-ducted as part of the Portsmouth NavalShipyard studies (Johnston et al., 1993).Initial measurements of metals in thePiscataqua River encountered problems,but samples of seep water from sitesnear suspected sources showed elevat-ed concentrations of Pb, Hg, Zn, Cr andCu, some of which may have beenassociated with suspended sedimentsinadvertently included in the samples.

Further sampling of the river and seepwaters were conducted as part of thesecond phase of the project (NCCOSC,1997). The data, when compared toWater Quality Criteria (WQC) for protec-tion of both human health and aquaticlife, showed measured contaminant con-centrations except for copper were >10xlower than the marine chronic WQCs. Allsites had copper concentrations ~10x

62

2.3

TOXIC ORGANIC AND METAL CONTAMINANTS

63

lower than the 3.1 mg/l WQC with thehighest concentration in the upperGreat Bay Estuary of 0.49 mg/l, which isonly ~6x lower.

NHDES measured concentrations ofAl, Cu, Zn and Pb that exceeded stan-dards in water samples from urban areasin the Lamprey River (NHDES, 1994b).They compared concentrations fromsamples in 1987-92 at rural sites withsamples from 1992 and 1993 at urbansites. The results indicated that the met-als were present at concentrations higherthan elsewhere in New Hampshire. Thereport recommended more intensivemonitoring for metals in the LampreyRiver and in other rivers to help put theresults into a broader context. In addi-tion, toxicity assessments in trouble areaswere also recommended. In follow-upstudies, the NHOSP found Al, Zn and Cuconcentrations in water samples from theExeter River to be greater than state stan-dards at many sites during storm events(NHOSP, 1995a), and frequent excee-dences for Pb, Zn and Cu during stormevents at numerous sites in the OysterRiver watershed (NHCP, 1996). Elevatedconcentrations of trace metals instormwater runoff in Dover and Exeterhave been measured, especially duringsignificant storm/runoff events (Jones etal., 1999).

It appears that tributaries to estuarinewaters have storm-related problems withtrace metal contamination. In addition totheir impact in the freshwater tributaries,the contaminants potentially may betransported to estuarine waters and poserisks to estuarine biota. The high copperconcentrations in the tributaries and inthe upper Great Bay Estuary are goodevidence that transport is occurring.

2.3.2 STATUS AND TRENDS FOR CONTAMINATED SEDIMENTS

Many studies have focused on contami-nants in sediments in coastal New Hamp-shire. Recent efforts are providing anupdate to many areas not surveyed sincethe 1970s (Bonis and Gaudette, 1998). Acomprehensive database for contaminat-ed sediments in coastal New Hampshireareas has been compiled by the USGS

and will soon be available on CD andthrough the Internet (Buchholtz tenBrink et al., 1994 & 1997). Data from thePNS estuarine ecological risk assessment(Johnston et al., 1994), the Army Corpsof Engineers dredging projects (NAI,1994) and various scientific papers, con-sulting firm reports and theses areincluded. In all, the database includesdata for 199 samples from New Hamp-shire, 452 samples from Maine and 993samples from USACE permit applicationsand federal navigation projects. Informa-tion in the database is from reports andpapers dating from 1973 to 1994, provid-ing the opportunity in the future todetermine trends for sediment contami-nants at specific sites. The data, alongwith data from the rest of the Gulf ofMaine, are presently being validated andinterpretive maps are being produced.

The trace metal at highest concentra-tion in New Hampshire’s estuarine sedi-ments is chromium. The range ofchromium concentrations in sediments is12-2300 mg/l. The highest chromiumconcentrations are found in the CochecoRiver, where tannery waste with highlevels of chromium were discharged.Chromium concentrations in CochecoRiver sediments are commonly greaterthan the ER-M of 145 mg Cr/l. Chromiumfrom the Cocheco River has been trans-ported throughout the estuary (Capuzzoand Anderson, 1973).

Examples of the latest draft versions ofthe USGS maps for New Hampshire arepresented in Figures 2.21-23 for mercury,lead and chromium, along with an exam-ple map of lead concentrations in the USportion of the Gulf of Maine (Figure2.24) to provide a regional perspective toNew Hampshire data. Data and maps arealso available for nickel, cadmium, zinc,copper, phenanthrene, fluoranthene andpyrene in both the Gulf of Maine and inthe Great Bay Estuary. The three examplemaps presented are useful to see generalpatterns in contaminant concentrations.The data are comprehensive and do notdistinguish between older and newerdata, analytical methods, sampling meth-ods, or sample replication. Validation ofdata and maps is ongoing, along with the

64

Mercury Concentrationsin Sediments 1973-1994

0.71 to 68.8 0.15 to 0.71 0.06 to 0.15 0 to 0.06

FIGURE 2.21

Mercury concentrations in sediments in coastal New Hampshire waters:1973-1994.

FIGURE 2.22

Chromium concentrations in

sediments in coastalNew Hampshire

waters: 1973-1994.

65

370 to 7,140 µg/g 81 to 370 µg/g 70 to 81 µg/g 0 to 70 µg/g

Chromium Concentrationsin Sediments 1973-1994

66

Lead Concentrationsin Sediments: 1973-94

218 to 7,000 µg/g

46.7 to 218 µg/g

35 to 46.7 µg/g

0 to 35 µg/g

FIGURE 2.23

Lead concentrations in sediments in coastalNew Hampshire waters: 1973-1994.

67

databases for organic contaminants andsediment texture.

Figure 2.21 shows numerous sites inthe lower Piscataqua River and Rye Har-bor that have Hg concentrations thatexceed the ER-L sediment quality criteri-on of 0.15 µg/g (Long and Morgan,1990), but no sites that exceed the ER-Mcriterion of 1.3 µg/g. The upper GreatBay Estuary generally had lower levels ofmercury. Sites with lead concentrationsthat exceed the ER-L criterion of 35 g/gare numerous and spread throughout theentire coastal New Hampshire area (Fig-ure 2.22). Three sites had lead concen-trations greater than the ER-M level of110 µg/g. The sites were near SeaveyIsland in Portsmouth Harbor and in theSquamscott River. Many sites with lowerconcentrations (<31 µg/g) were concen-trated around Adams Point and Little Bayareas. Only four sites had concentrations

of copper at or near the ER-L concentra-tion of 70 µg/g. The sites included thesame two sites that had high lead con-centrations near Seavey Island, and twoother sites in Great and Little bays. Rela-tively high (>81 µg/g) chromium con-centrations are spread throughout theGreat Bay Estuary (Figure 2.23), with thehighest concentration in the CochecoRiver. The Gulf of Maine map presentslead concentration in relation to back-ground concentrations (20 µg/g), withvalues up to 2-3 orders of magnitudegreater than background (Figure 2.24).Only one site (near Seavey Island) had aconcentrations as high as 2.5 orders ofmagnitude greater than background.

As a means of assessing the impact ofoil spills on sediments, sediments werecollected monthly at 24 intertidal andsubtidal sites throughout the Great BayEstuary and analyzed for hydrocarbons

Lead Concentrations (ppm) ≥ 100 30 to 100

10 to 31 ≤ 10

FIGURE 2.24

Lead concentrations in sediments in the U.S. portion of the Gulf of Maine and

Georges Bank.

(Nelson, 1982). Nelson (1982) reportedthe results of analyses for PAHs and alka-nes for February, 1981 at both intertidaland subtidal sites at eight different sta-tions. Concentrations were reported for13 different PAHs, ranging from 0 fornumerous PAHs to >1000 mg/g sedimentfor chrysene and benzo[a]anthracene atNobles I., Cedar Pt., Royall’s Cove andFox Pt. Alkane analysis was reported asconcentrations for even and odd-num-bered carbons in chains ranging from 14to 32 carbons. Total alkane concentra-tions ranged from 707 ng/g sediment to24,960 ng/g sediment. Sites with the

highest concentrations included RollinsFarm (>14,800 ng/g), Broad Cove(>17,000 ng/g) Royall’s Cove (>24,900ng/g) in either intertidal or subtidal sites.Evidence of contamination from oil spillswas evident at all sites, suggesting thatoil spilled mainly in the lower estuary islikely transported to the upper estuary.

Dredge materials in New Hampshirehave been disposed of in intertidal,nearshore, open water, upland orunknown locations (NAI, 1994). Much ofthe material dredged was disposed of atthe Cape Arundel open water site. Someof the Rockingham County material was

68

≥ 500 100 to 500

.01 to 100 < .01

PCB Concentrations inSediments: 1973-1994

FIGURE 2.25

PCB concentrations in sediments in coastalNew Hampshire waters: 1973-1994.

2.3.3 SOURCES OF TOXIC CONTAMINANTS

Current industrial discharges of toxic con-taminants are significantly less than thehistorical discharges that are probably thecause of much of the existing contami-nants in New Hampshire sediments. Mostcurrent sources of toxic contaminants aresuspected to be more diffuse sourcessuch as urban stormwater runoff, atmos-pheric deposition, oil spills, and runoffplus groundwater infiltration from Super-fund sites, golf courses and landfills.Stormwater runoff is the most frequentlycited existing source of toxic contami-nants in coastal New Hampshire (Jones etal., 1999). Stormwater runoff and associ-ated storm event effects may alsoenhance contamination for some of theother sources of contaminants detailedbelow.

2.3.3.1 Stormwater Runoff

Stormwater runoff is the most frequentlycited existing source of toxic contami-nants in coastal New Hampshire. Signifi-cantly elevated concentrations ofaluminum, lead, copper and zinc havebeen documented in freshwater tributar-ies (NHDES, 1994; see Status and Trendsof Contaminants in Water section). Muchof the stormwater and associated con-taminants probably enter surface watersvia stormdrains in urban areas (Jones etal., 1999; Jones, 1998b; Landry, 1997).This is currently the focus of a study sup-ported by the NHCP. Stormwater is alsosuspected to enter the Great Bay Estuarydirectly through various streams andbrooks throughout each bordering town.The area around the former Pease AirForce Base (PAFB) has been well docu-mented. There are two drainage streamsin Newington that are permitted NPDESoutfalls, both formerly used by PAFB andpresently used by the Pease InternationalTradeport (Figure 2.26). Flagstone Brookflows north from the site and eventuallydischarges into lower Little Bay (TrickyCove) while McIntyre Brook flows fromthe runway into southeastern Great Bay.Both brooks are used for disposal of“stormwater runoff from airport activities”

according to the NPDES, EPA-issued per-mit. Activities resulting in the productionof this waste include aircraft mainte-nance, aircraft fueling, painting and strip-ping, aircraft washing and mostsignificantly, aircraft de-icing. McIntyreBrook has the potential for having a moredirect impact on the growing area thanFlagstone due to the location of the dis-charge relative to shellfish resource areas.Major effluent characteristics that requiremonthly monitoring in McIntyre Brookinclude pH, oil and grease, primary de-icing chemical, surfactants, trichloroethyl-ene (quarterly), and total recoverable ironand zinc. Most of the runway and aircraftparking apron, industrial shop area andthe entire flightline area drain into McIn-tyre Brook. There is an oil/water separa-tor located near the origin of McIntyreBrook and a newly installed separator onFlagstone Brook. One of the main con-cerns with McIntyre Brook has been thepropylene glycol content in the dis-charged water. This product is used indeicing aircraft and can potentiallydecrease the amount of dissolved oxygenin water. In 1992, as a part of the AirForce Installation Restoration program,shellfish tissue analysis was performed onsamples collected in the vicinity of the AirForce Base. In an effort to evaluate thepotential impacts of contaminantsreleased from the Air Force Base intoMcIntyre Brook, American oysters, soft-shell clams, ribbed mussels and mummi-chogs were collected at the mouth of thebrook where it discharges into Great Bay.Results of these analyses concluded thataluminum, arsenic and potassium con-centrations in shellfish tissue samplesexceeded background concentrations.However, the presence of these metalsand the concentrations in which theywere detected, do not pose a significanthealth risk to humans and were not con-cluded by the NHDES to be potentialhealth risks.

In addition to McIntyre and Flagstonebrooks, there are two non-permitteddrainage brooks located on the PeaseInternational Tradeport property whichdrain into the southeast portion of GreatBay. They are Peverly Brook and Picker-

70

71

ing Brook. Runoff is characterized pre-dominantly by overland flow to thesestreams. The Pease International Trade-port has adopted a Stormwater BestManagement Practices Plan in order toproperly handle all stormwater wasteoriginating at the facility.

A joint UNH-JEL/NHDES study onstormwater control systems in the coastalarea assessed the effectiveness of the sys-tems to remove Al, Cd, Cu and Zn (Jonesand Langan, 1996b). Concentrations ofAl, Cu and Zn in the effluent from all ofthe systems exceeded the New Hamp-shire acute water quality standards forprotection of aquatic life (NHDES,1996b) during at least one storm event,especially during storms that occurred inwinter. Cadmium concentrations rarelyexceeded the acute standard, andexceeded the chronic standard less fre-quently than for other metals.

2.3.3.2 Superfund Sites

There are Superfund sites in coastal NewHampshire (Figure 2.27) with thePortsmouth Naval Shipyard, the formerPease Air Force base and Coakley land-fill being of most concern to estuarineenvironmental quality. Copious amountsof information have been generated onenvironmental concentrations of contam-inants, cleanup strategies, and toxicity tobiota for both the Portsmouth NavalShipyard (NCCOSC, 1997; Johnston et al.,1994) and the former Pease Air ForceBase (Earth Tech, 1995). A large numberof studies for these sites have beenreviewed and synthesized (NCCOSC,1997; Earth Tech, 1995).

At PAFB, elevated concentrations ofcontaminants have been found in thesediments of some small streams, ingroundwater plumes, in some biota, and

Superfund Sites

FIGURE 2.26

Superfund sites and surface waters

in the former Pease Air Force base.

72

Superfund Sites

FIGURE 2.27 Superfund sites in the coastal region of New Hampshire.

73

in soil (Weston, 1992), mostly in closeproximity to known sites of hazardouswaste storage, disposal or discharge.Extensive measurements of contaminantsin surface water, sediments and fish havebeen made (Weston, 1992). In addition,extensive analysis of surface water at twosmall rivers and sediments at three wet-lands, all considered to be unimpactedby pollution, were conducted to estab-lish naturally occurring background con-centrations of contaminants as a basis forestablishing remediation goals for Pease(NHDES, unpublished data). Elevatedconcentrations of DDT compoundsreflect local deposition or applicationprobably from the 1950s and 1960s(Weston, 1994). Detailed summaries ofenvironmental factors at each of 48Installation Restoration Program siteshave been compiled (USAF, unpublishedreport). On the basis of extensive assess-ments of sediment and water contami-nant analysis and toxicity assays,remedial alternatives for sediments wereevaluated (Weston, 1996). Cleanup andremediation of stream sites with contam-inated sediments include Paul’s andMcIntyre brooks, which had elevatedconcentrations of pesticides, metals andPAHs of concern to ecological receptors,though not to humans (USAF, 1997).Contaminants in Lower Newfields Ditchand Flagstone Brook have been deter-mined to pose no risk to humans or eco-logical receptors, and no further actionhas been recommended.

The Coakley Landfill is located inNorth Hampton 6 miles up the freshwa-ter portion of Berry Brook. It receivedmunicipal and industrial wastes from thePortsmouth and Pease Air Force Basearea between 1972-1985. In 1983, theNHDES found groundwater and surfacewater contamination with volatile organ-ic compounds (VOCs) at numerous sitesin the area (see Hughes and Brown,1995). The site was added to the USEPANational Priority List in 1983, rankednumber 680. The site has undergoneremediation, yet VOCs are still beingdetected in some locations near the land-fill (1993 EPA data). This became a con-cern to the Town of Rye and they

undertook a small investigation of waterquality along the whole length of BerryBrook. They sampled twice during thespring of 1995, and had samples from 9sites along the stream, from the CoakleyLandfill to the Estuary, analyzed for awide range of contaminants (Hughes andBrown, 1995). These included 10 metals,60 VOCs, 20 pesticides and 7 PCBs.None of the toxic organic compoundswere detected in any sample. The metalswere all present at low concentrations orundetectable. They found dissolved oxy-gen to be low near the landfill, but satis-factory at other sites. Suspended solids,dissolved inorganic nitrogen and phos-phorus, and fecal indicator bacteria con-centrations were all low.

Other Superfund sites are locatedwithin close proximity to the Great BayEstuary. The Tolend Road site in Dover islocated near the upstream portion of theBellamy River. The Somersworth landfillis located near the Salmon Falls River.

2.3.3.3 Documented Groundwater Pollution Sources

Landfills, fuel storage, hazardous wastegenerators and documented groundwa-ter pollution sources are all in GIS on theGRANIT system (Figure 2.28). A recentcompilation of landfills located withinthe Great Bay Estuary watershed wasprovided by NHDES, and is presented inTable 2.5. Most of the landfills have aGroundwater Management Permit. Thisrequires leachate monitoring, and infor-mation on flow and analytical composi-tion are routinely submitted to NHDESfor review.

Pease InternationalTradeport

74

TABLE 2.5 Conditions and characteristics of active and closed landfills in the coastal region of New Hampshire.

Town Location Start-up1 Active vs Lined vs Leachate HydraulicClosed Unlined Monitored2 Connection

Barrington Smoke St. Early 1950s Inactive since 1980 Unlined Yes

Brentwood NO MSW 3 N/A N/A NIA N/A N/A

Brookfield NO MSW N/A N/A N/A N/A N/ALANDFILL

Candia New Boston Rd. Inactive Unlined Yes

Chester Route 102 Mid. 1950s Active Unlined Yes

Deerfield Brown Rd. 1970s Closed4 1996 Unlined Yes

Dover Toland Road 1960 Inactive Unlined Yes

Durham Durham Pt. Rd. 1950 Inactive Unlined Yes Adjacent to Horsehide Brook

East Kingston NO MSW3 N/A N/A N/A N/A N/ALANDFILL

Epping Old Hedding Rd. Inactive Unlined No

Exeter Cross Rd. 1976 Closed 1995 Unlined Yes

Farmington Watson 1940s Active Unlined Yes Water flowsCorner Rd. toward the(Municipal) Cocheco R.

Watson Late 1960s Inactive Unlined Yes Water flowsCorner Rd. (Cardinal toward the(Private) Landfill) Cocheco R.

Fremont Danville Rd. 1960s Inactive Unlined Yes Is adjacent tosince 1978 the Exeter R.

Greenland Cemetery Ln. Pre. 1900 Inactive Unlined No

Hampton Tide Mill Rd 1963 Closed 1996 Unlined Yes

Hampton NO MSW N/A N/A N/A N/A N/AFalls LANDFILL

Kensington NO MSW N/A N/A N/A N/A N/ALANDFILL

Kingston Route 125 1920s Active Unlined Yes

Lee Mast Rd. Inactive Unlined

Madbury Route 155 Late 1970s Closed1 1995 Unlined Yes(Madbury Metals)

Middleton NO MSW N/A N/A N/A N/A N/ALANDFILL

New Castle NO MSW N/A N/A N/A N/A N/ALANDFILL

New Durham Old Rte 11 Early 1970s Inactive Unlined No

75

Conditions and characteristics of active and closed landfills in the coastal region of New Hampshire (continued).

Town Location Start-up1 Active vs Lined vs Leachate HydraulicClosed Unlined Monitored2 Connection

Newfield NO MSW N/A N/A N/A N/A N/ALANDFILL

Newington Pease Tradeport Mid. 1950s closed6 1996 Unlined Yes

Newmarket Ash Swamp Rd 1950 Closed 1995 Unlined Yes

Northwood Route 4 Inactive Unlined No

North Coakly 1972 Inactive closure Unlined YesHampton Superfund Site expected 1997

Nottingham Freeman 1973 (Ash Pile] Unlined NoHall Rd ActiveFreeman 1960s Active8 Unlined Yes

Portsmouth Mirona Rd 1950s Inactive Unlined NoJones Ave. 1940s Closed 1991 Unlined YesAsh LF

PSNH Schiller Sta Closed 1980s Unlined YesWoodbury Ave

Raymond Prescott Rd. Closed Unlined Yes

Rochester Turnkey LF 1980s Active Double Lined Yes

Old Dover Rd Closed 1980s Unlined Yes

Rollinsford NO MSW N/A N/A N/A N/A N/ALANDFILL

Rye Breakfast Hill Rd Closed 1988 Unlined YesGrove Rd Inactive Unlined Yes

Sandown NO MSW N/A N/A N/A N/A N/ALANDFILL

Seabrook Rocks Rd. Inactive Unlined No

Sommersworth Blackwater Rd. 1930s Inactive Unlined YesSuperfund Site

Strafford Nelson Rd. Inactive Unlined No

Stratham Union Rd. 1950s Closed 1995 Unlined Yes

Wakefield Route 153 1974 Active Unlined Yes

1. A blank box indicates there is insufficient information on file to determine the date the landfill began accepting waste.2. Leachate is monitored by the use of groundwater monitoring wells and surface water stations a: the landfill site.3. MSW = Municipal Solid Waste.4. Closed = Closed in accordance with State approved test” plans.S. The Madbury Metals landfill c contains automobile shredder residue.6. There were a total of five MSW, three Construction/Rubble Dump landfills and one paint can disposal area at the former Pease Air

force Base. Four MSW landfills were combined and closed as one site, while the fifth is a stump disposal area which is inactive. Two ofthe Rubble Dumps and the Paint can area continue to be monitored.

7. A file review proved inconclusive on whether PSNH had received state approval for the landfill closure design.8. The landfill in Nottingham is ~ construction and demolition debris landfill.

76

Hazardous Waste Sites

FIGURE 2.28 Hazardous waste sites and landfills in the coastal region of New Hampshire.

77

2.3.3.4 Oil Spills

There have been many oil spills of awide range of volumes in coastal NewHampshire. During 1975-79 there were103 oil spills in public waters in the 17coastal communities (SRRC, 1981). Themost significant spills included the tankerAthenian Star (10,000 gallons of dieselfuel) in 1975, Bouchard Barge #105 (8000gal. #6 fuel oil) in 1978 and the tankerNew Concord (25,000 gal. #6 fuel oil) in1979, mostly associated with the oil ter-minals in Portsmouth and Newington onthe Piscataqua River. Even though small-er spills were more frequent (94), ninespills of >500 gallons constituted 95.3%of the spilled oil. The impacts of the oilspills included fouling of beaches, shore-lines, boats, docks, fishing gear and lob-ster traps. Many people reported that theshellfish beds in front of their houseswere destroyed and that the marsh grassalong the shoreline was removedbecause it trapped and retained oil.Many claims filed by lobstermen andshoreline residents were still pending ayear and a half after some spills.

A 1981 NHF&G study (Nelson, 1982)was done specifically to serve as a base-line for assessing future oil spill impactsto estuarine resources. As a means ofassessing the impact of oil spills on sed-iments, sediments were collected month-ly at 24 intertidal and subtidal sitesthroughout the Great Bay Estuary andanalyzed for hydrocarbons. Nelson(1982) reported the results of analysesfor PAHs and alkanes for February, 1981at both intertidal and subtidal sites ateight different stations. Concentrationswere reported for 13 different PAHs,ranging from 0 for numerous PAHs to>1000 ng/g sediment for chrysene andbenzo[a]anthracene at Nobles I., CedarPt., Royall’s Cove and Fox Pt. Alkaneanalysis was reported as concentrationsfor even and odd-numbered carbons inchains ranging from 14 to 32 carbons.Total alkane concentrations ranged from707 ng/g sediment to 24,960 ng/g sedi-ment. Sites with the highest concentra-tions included Rollins Farm (>14,800ng/g), Broad Cove (>17,000 ng/g) Roy-

alls Cove (>24,900 ng/g) in either inter-tidal or subtidal sites. Evidence of con-tamination from oil spills was evident atall sites, suggesting that oil spilled main-ly in the lower estuary was likely trans-ported to the upper estuary.

At the present time, NHDES keepsrecords of all oil spills, including thosethat are spilled into surface waters.NHDES also has an oil spill clean up pro-gram. The NH Coastal Program keepsrecords of oil spills in the communitiesincluded on the coastal program.

The most recent significant oil spill inthe coast of New Hampshire occurred inthe Piscataqua River on July 1, 1996. Itinvolved a spill of ~1,000 gallons of #6fuel oil from the vessel Provence. Thevarious types of compounds in the oilhad different dispersion behavior, withsome oil sinking and other fractions float-ing. The floating oil was collected alongthe shoreline of Little Bay, and the por-tion that sank is probably now associatedwith Little Bay sediments. Much of the oilsank in Little Bay, and the impact to biotawas under investigated (NHF&G, 1996).Chase et al. (1997; 1998) reported elevat-ed concentrations of PAHs in blue mus-sels at Dover Point 16 days after the spillin comparison to 1994 concentrations(Chase et al., 1996a). Low molecularweight PAHs decreased in concentrationor disappeared in samples collected threeand fifteen months after the spill, butconcentrations of high molecular weight(> 5 rings) PAHs persisted and were stillsignificantly higher than in 1994 tissue.Samples of both blue mussels and oystersfrom Fox Point collected 16 days after thespill had concentrations of PAHs approx-imately twice as high as seen at DoverPoint. This difference is probably a func-tion of where the oil was eventuallydeposited after initial transport via watercurrents soon after the spill.

In 1998, the NHDES joined efforts withthe Gulfwatch program through UNH/JELto expand the use of monitoring bluemussel tissue for toxic contaminants inNew Hampshire waters (Jones andLandry, 2000). One key goal is to establisha baseline of data that could be used tomonitor recovery in the event of a future

oil spill. New monitoring sites have beenestablished that bracket the major oil stor-age and off-loading facilities on the Pis-cataqua River and in other areas of theestuary that could be impacted by spills.

2.3.3.5 Fertilizer and Pesticide Applications

Historically, agricultural activities areassociated with significant fertilizer andpesticide applications. The small numberand sizes of crop-producing farms incoastal New Hampshire make agricultureless significant, and the contributions ofgolf courses and residential lawns hasbecome relatively more significant. Useof all types of pesticides in Rockinghamand Strafford counties has increasedsince 1965 (NHCRP, 1997). In 1994,281,706 lbs of >250 pesticides were usedin NH, with 1,000 to 10,000 lbs/y in estu-arine drainage areas.

There are at least ten golf courses inthe coastal communities of New Hamp-shire. Many are inland, but a few are inclose proximity to estuarine surfacewaters. All golf courses need to use fer-tilizers and pesiticides to maintain thehigh quality turf on fairways and greens.Pesticides transported to estuaries viarunoff or groundwater can cause harm tonon-target estuarine organisms. Pesticideuse at NH golf courses is regulatedthrough a New Hampshire PesticideBoard (Department of Agriculture) per-mitting process. A survey of groundwatersamples from 25 shallow wells at agri-cultural sites and golf courses, some ofwhich were in the coastal area, showedno detectable pesticides, and metal con-centrations were all within drinkingwater standards (NHDHHS, 1986).

Runoff and groundwater can also con-tain nutrients from fertilizers that maycontribute to nutrient overenrichment. Adrainage swale downgradient from theRockingham Country Club in Newmarkethad the highest loading rate for nitrate(~2.7 kg nitrate/d during high flow) thanany other tributary to the SquamscottRiver (Jones and Langan, 1995c). Possi-ble upstream sources were investigatedand no significant source other than thegolf course was apparent.

The Wentworth-by-the-Sea golf courseuses a number of strategies to managefertilizer and pesticide applications andminimize environmental impact becausethey use both on land that is immediate-ly adjacent to Little Harbor (Rye-Went-worth Impact Assessment Report, 1990).A slow-release fertilizer (24-4-12) isapplied to fairways, tees and greens inMay, June and September at annual ratesranging from 130-218 lbs/acre of nitro-gen and 22-36 lbs/acre phosphorus.Roughs are not fertilized. Grass clippingsare returned directly (mulched) onto fair-ways. Tee and green clippings are col-lected and spread on the roughs. Watersample analysis suggested that the fertil-izers applied at the course have littleimpact on the water quality of the harbor(Jones and Langan, 1995c). Insecticidesare not used routinely or on a large scale.Instead, an integrated pest managementsystem is employed and pesticide appli-cation is limited to spot application tocontrol grub infestation. Preventativetreatment for snow mold fungus isapplied only to tees and greens. Heavymetal (mercury) based compounds arenot used. All materials are applied con-servatively with particular caution paid toadjacent surface waters and wetlandbuffer zones. Equipment used for appli-cations is field-rinsed, and the dilutedrinse water is sprayed onto the fairwaysto prevent a large volume of this waterbeing washed into maintenance facilitystorm drains (Rye-Wentworth ImpactAssessment Report, 1990).

Some other golf courses are in rela-tively close proximity to estuarine watersand tributaries. Portsmouth Country Clubis located in Greenland on the southeast-ern shore of Great Bay, the Rochester,Farmington and Cocheco country clubsare near the Cocheco River, the ExeterCountry Club is near the SquamscottRiver, and Pease Golf Course is near theshores of Great Bay.

Within salt marshes, human nuisancessuch as mosquitos and green-head fliesare managed by seacoast towns that col-lectively spend approximately $100,000each year (USDA 1994); ironically, most ofthe effort to control these pests occurs in

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degraded marshes (see habitat loss sec-tion). The NH Division of Pesticide Controlhas provided information on the coastaltowns involved and the major contractors.The towns include Newcastle, Newfields,Stratham, Hampton Falls, Portsmouth,Hampton, Rye, Newmarket, Exeter, New-ington, Seabrook and the Great BayNational Refuge. The towns conductintegrated systems of control, using bothadulticiding and larviciding techniques.Insecticides used include GB-111 andVectoBac 12AS, CG and G. The larvicidalinsecticides used typically depend on theactivity of the bacterium Bacillus thurin-giensis var. israelensis, and the adulti-cides are often pyrethroids.Organophos-phate insecticides are also used.

2.3.3.6 Atmospheric Deposition

In an effort to refine and regionally focusthe issue of atmospheric deposition ofmercury, representatives of the regionsstate air, water, waste and public healthdivisions and Environment Canadaformed a Mercury Workshop. This grouprecently published their findings(NESCAUM, 1998). The Workshop con-cluded that about 47% of mercury depo-sition in the region originated fromsources within the region, 30% from U.S.sources outside the region, and 23% fromthe global atmospheric reservoir. Thisreport has provided the impetus for aconcerted regional effort to reduce mer-cury emissions. On June 8, 1998, theNew England governors and easternCanadian premiers agreed to cut region-al mercury emissions from power plants,incinerators, and other sources in half bythe year 2003 (Boston Globe -6/9/98).

The USEPA has monitored 70 toxicvolatile compounds, including 56 volatileorganic compounds (VOC) atPortsmouth and three other sitesstatewide since 1989 (NHCRP, 1997).Anthropogenic sources of VOCs includeindustrial processes, solvents, oil-basedpaints and automobiles. In 1994, the vol-ume decreased to 23,174,000 tons, downfrom 30,646,000 tons in 1970. Most of thereduction came from automobiles, as theamount decreased from 12,972,000 to6,295,000 from vehicles. Of the 70 com-pounds monitored, 37 have disappeared

since 1987, and 15 have decreased inconcentration.

A summary of recent existing inputand output data for four inorganic andnine organic contaminants in the Gulf ofMaine identified major data gaps in thecurrent understanding of atmosphericdeposition of contaminants (McAdie,1994). Numerous papers were presentedat a recent conference on regionalatmospheric Hg deposition (EMAN,1996). Gaseous mercury concentrationsin the atmosphere over the Gulf of Mainewere reported to range from 0.4 to 2.0ng/m3. The concentrations generallyvary inversely with altitude. Municipaland medical waste incineration is proba-bly a significant localized (30-50 mileradius) source of Hg deposition in NewHampshire. In Maine, measurements ofmercury in rain and snow showed rangesof 5-15 ng/L, giving wet deposition val-ues of about 6-10 µg/m2/y. A newatmospheric monitoring station has beenestablished at Newcastle, NH. Data col-lected are providing information onatmospheric mercury deposition in thecoastal New Hampshire area as part ofthe national Mercury Deposition Net-work (MDN). Comparison with an inlandMDN site at Laconia, NH, suggested thatNew Castle may be receiving greatermercury deposition than inland areas,along with other coastal sites in newEngland (VanArsdale et al., 1998).

2.3.3.7 Summary

Aside from historically resuspended con-taminated sediments, the most significantdocumented sources of contaminants arestormwater runoff, oil spills and Super-fund sites located adjacent to the GreatBay Estuary. All three source categoriesare receiving attention by state, federaland private agencies to mitigate contam-ination in the remaining source areas ofNew Hampshire. For some contaminantslike mercury, atmospheric deposition issuspected to be a significant source, butis at present not well documented. Con-tinued reductions of external sources ofcontaminants is important because of theexistence of elevated contaminant con-centrations from historical sources insome areas.

2.3.4 CONTAMINANT AND HYDRODYNAMIC MODELING

Mathematical computer modeling of cir-culation and tidal flow in the Great BayEstuary was first done in the 1970s(Celikkol and Reichard, 1976; Brown andArellano, 1979). The early two dimen-sional model examined the movement ofwater up the main stem of the Estuaryand calculated the flushing time and tidalexchange for the various parts of theestuarine system (Swift and Brown, 1983;Short, 1992b). More detailed two dimen-sional models have been developed toexamine the path that oil might take if aspill were to occur in the Estuary (Swiftand Celikkol, 1983). The primary focusof the oil spill model was on the Pis-cataqua River near the oil loading termi-nals. The model included the upperEstuary, but it was never calibrated forGreat Bay proper.

Recent efforts have begun to modelthe hydrodynamics and current flowpatterns in Great Bay proper as part ofan effort to develop modeling capabili-ties for simulating hydrodynamic flowsin estuaries having intertidal areas (Ip etal., 1997). This model provided the firstdetailed hydrodynamic assessments forGreat Bay and successfully simulatedthe movement of water on and off theextensive intertidal mudflats within thatsystem. This two dimensional finite ele-ment model for Great Bay, currentlyunder development at Dartmouth Col-lege, produces fine scale output of cur-rent velocities and tidal variations withinGreat Bay and upper Little Bay. Theproblems of model simulation withinintertidal estuaries have been resolved,but the Great Bay model has not yetbeen field verified.

A finite element, two dimensionalhydrodynamic model has been adaptedto the entire Great Bay Estuarine systemas part of the US Navy Ecological RiskAssessment Study (Pavlos, 1994). TheWASP4 model, originally developed bythe EPA, was used to estimate the distri-bution of lead throughout the Great BayEstuary, assuming discharges wereoccurring at the Portsmouth Naval Ship-

yard (Chadwick, 1993; Pavlos, 1994). Themodel includes the simulation of dis-solved substances within the water col-umn throughout the lower portions ofthe Estuary (TOXIWASP, Pavlos, 1994).The TOXIWASP model was used toexamine salinity distribution as well. Thedevelopment of an improved version ofthe WASP model and the need for betteraccuracy in model predictions lead to theapplication of the WASP5 model to theGreat Bay Estuary and a series of simula-tions, again looking at the transport oflead from sources around the shipyard aswell as sources elsewhere in the Estuary(Scott, 1997). The focus of the WASP5model was the Piscataqua River andPortsmouth Harbor although it was fit tothe entire Estuary. This model was suc-cessful in predicting the transport of leadthroughout the lower part of the Estuaryand in determining sites where elevatedconcentrations of lead might accumulate.

WASP has recently been used tomodel nonpoint source pollution in thetidal portion of the Oyster River (Swift etal., 1996). Different programs withinWASP were used to model currents andwater levels, salinity, bacteria, nutrientsand dissolved oxygen. The model exer-cise found that the flushing time of theriver is 3 days. The model was also usedto simulate contaminant distributions foran effluent release from the DurhamWWTF, a significant rainfall event, and foraverage conditions. The results were rel-atively effective for simulating trends andprocesses when compared to field datacollected as part of two previous studies(Jones and Langan, 1993a, 1994c).

WASP was also used by the State ofMaine (Mitnick, 1994) to determine thereduction in phosphorus from WWTFrequired to meet the strict Maine WQCsfor chlorophyll in the freshwater portionsof the Salmon Falls River. The majorWWTF included were at Berwick, MEand Somersworth, NH. The results sug-gested drastic reductions in phosphorusdischarges would be needed. Experi-mental reductions in phosphorus at theWWTF confirmed that reductions inchlorophyll in the freshwater portion ofthe river were possible (Mitnick, 1994).

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2.3.5 PUBLIC HEALTH RISKSAND ECOLOGICAL IMPACTS

New Hampshire coastal waters are pop-ular areas for commercial and recre-ational fishing and recreationalshellfishing. In addition, the area isnoted and valued for its relatively pris-tine conditions, and the ecologicalintegrity of the coast is an importantresource. One threat to both publichealth and ecosystem integrity is thepresence of toxic contaminants. TheNHDHHS and other state agencies mon-itor contaminants and assess the risks tohumans. They provide direct access toconsumption advisory information via 1-800-852-3345 ext. 4664. At present, thereare advisories based on elevated Hg ininland lakes and rivers, and two advi-sories in New Hampshire related to con-sumption of marine fish, both based onelevated PCBs (Table 2.6; NHDES,1996b). These advisories are based on

three studies conducted more than nineyears ago. One of the first studies forshellfish from coastal New Hampshirewas by Isaza et al. (1989). The resultssuggested that lead, PCB and PAH con-centrations were elevated and warrantedfurther study. To further determine howshellfish may impact human health,another study was conducted by NHD-HHS (Scwalbe and Juchatz, 1991). As aresult of the PCB concentrations foundin lobster tomalley in their study, DHHSissued a consumption advisory for lob-ster tomalley in the Great Bay Estuary.There was also an advisory for con-sumption of coastal bluefish in NewHampshire issued in 1987 because ofelevated PCB concentrations found inbluefish from sites along the AtlanticCoast (NOAA, 1987). These advisoriesare thus based on small, relatively olddatabases. More recent studies have pro-vided newer and more comprehensiveinformation on tissue body burdens of

Who We’re SpeciesConcerned About of Concern Recommendations

General Advisory For All • Women of reproductive age All species Limit to one 8-oz. meal per monthInland Freshwater Bodies

• Children 6 years of age or younger All species Limit to one 3-oz meal per month

• All other consumers All species Limit to four 8-oz meals per month

Androscoggin River • Pregnant and nursing women All species Avoid consumption(from Berlin tothe Maine border) • All other consumers All species Limit to one or two 8-oz. meals/year

Great Bay Estuary • Pregnant and nursing women Lobster Limit consumption; avoid tomalleyBluefish Avoid consumption

• Children under 15 Lobster Limit consumption of tomalleyBluefish Avoid consumption

• All other consumers Lobster Limit consumption of tomalleyBluefish Avoid fish over 20 in. or 4 lbs;

prepare according to guidelines

Connecticut River • All consumers All species Prepare according to guidelines

Horseshoe Pond • All consumers Largemouth Avoid consumptionBass

Recommended consumption advisories for fish from the New Hampshire Department of Healthand Human Services. From NHDES (1996b).

TABLE 2.6

contaminants for a variety of animal andplant species.

Contaminant concentrations in bluemussels, other shellfish, lobsters, winterflounder and marine plants have beenreviewed and summarized. The databaseavailable for blue mussels (Mytilus edulis)is the largest of any organism, with up to85 sample analyses for each contaminant(Table 2.7. A more detailed summary ispresented in Appendix H. Blue musselsare commonly used as an indicator forhabitat exposure to organic and inorgan-ic contaminants. Bivalves such as M.edulis have been successfully used asindicator organisms in environmentalmonitoring programs throughout theworld (NAS, 1980; NOAA, 1991; Widdowsand Donkin, 1992; O’Connor, 1992; O’Con-nor and Beliaeff, 1995; Widdows et al.,1995; Jones et al., 1998) to identify varia-tion in chemical contaminants amongsites and contribute to the understandingof trends in coastal contamination.

Blue mussels are a useful indicatororganism for the following reasons: theyare abundant within and across coastalNew Hampshire; they are easy and inex-pensive to collect and process; much isknown about mussel biology and physi-ology; mussels are a commerciallyimportant food source (although in NewHampshire there is only recreational har-vesting of mussels) and therefore a meas-urement of the extent of chemicalcontamination is of public health con-cern; adult mussels are sedentary, there-by eliminating the complications ofinterpreting results introduced by mobilespecies; mussels are suspension-feedersthat pump large volumes of water andconcentrate many chemicals in their tis-sues making it easier to detect trace con-taminants; and the measurement ofchemicals in bivalve tissue provides anassessment of biologically available con-tamination that is not always apparentfrom measurement of contamination inabiotic environmental compartments(water, sediment, and suspended parti-cles). They also have well-defined limita-tions. One limitation is that they are onlymildly tolerant of low salinities, and alter-native shellfish (oysters, clams) may be

required for areas such as Great Bay andsome tributaries where salinities can betoo low.

A summary of the data for mussels incoastal New Hampshire and nearbyareas in Maine and Massachusetts is pre-sented in Table 2.7. More detailed pres-entation of specific organic contaminantsis available in Appendix H and in thereports that served as sources of thisinformation. A series of “Guidance Doc-uments” have recently been publishedby the USFDA (1993) for cadmium,chromium, lead and nickel “alert” levels.The levels do not warrant issuance ofhealth advisories, but serve as useful tar-get concentrations for assessing potentialhealth risks from seafood consumption.The data in Table 2.7 show no metalother than lead came close to the alertlevels. Lead concentrations in musselsexceeded the guideline level of 11.5 µg/gdry weight in nine samples at five sitesaround Seavey Island in Portsmouth Har-bor and at one site in the Lamprey River.The highest concentration was 76 µg/g atHenderson Point on the southern end ofSeavey Island. The other sites with con-centrations >11.5 µg/g had values of12.0-32.4 µg/g.

In 1997, mussels from Rye Harbor,Dover Point and Clarks Cove on SeaveyIsland had greater tissue Hg levels (>0.64µg/g) than any of the other 22 sites mon-itored (Chase et al., 1998). An analysis ofthe Gulfwatch data from 1995 showedthat the highest concentrations of cadmi-um and chromium from amongst the 14sites monitored throughout the Gulf ofMaine were found in mussels fromDover Point (Chase et al., 1996). For thefirst five years, 1991-1995, samples fromShapleigh I., Dover Point and Clark Covehad the 2nd, 4th and 7th highest chromi-um concentrations in the Gulf of Mainefrom amongst 59 sites (Jones et al.,1998). Samples from the same three sitesand Little Harbor had amongst the topten concentrations in the Gulf of Mainefor lead, mercury, nickel, zinc, aluminumand iron, while the 1995 Dover Pointsample with a high cadmium concentra-tion was the highest in the Gulf for thefive year period.

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Blue mussels American oyster Soft shell clam Mytilus edulis Crassostrea virginica Mya arenaria

USFDA Tissue Tissue TissueAction Level Concentrations No. of Concentrations No. of Concentrations No. offor shellfish Average Range samples Average Range samples Average Range samples

Trace metals µg/g* µg/g µg/g* µg/g µg/g* µg/g

Ag 0.5 0.03 to 2.8 66 17.0 12.3 to 22.6 5 0Al 282 77 to 650 40As 8.5 5.1 to 13.5 36 6.5 4.1 to 10.1 13 20.6 20.6 1Cd 25 2.3 0.1 to 9.3 85 4.5 3.5 to 6.8 5 1.0 0.3 to 1.4 8Cr 87 5.1 1.5 to 57 85 2.7 1 to 4.5 15 11.1 4.3 to 26.7 8Cu 9.6 5.5 to 45.5 83 215 114 to 301 7 13.3 11 to 15 2Fe 572 209 to 1,300 46Hg 6.7 0.47 0.13 to 1.1 73 0.61 0.07 to 1.1 13 0.35 <0.2 to 0.42 9Ni 533 2.6 1.1 to 16.7 72 3.2 2.7 to 4.1 5 9.3 9.3 1Pb 11.5 8.4 1.9 to 76 85 2.2 0.61 to 5.2 17 13.1 5.6 to 36 9Zn 122 80 to 270 85 5383 3,770 to 6,000 7 70 59 to 80 2

Toxic Organics ng/g ng/g ng/g ng/g ng/g ng/g

PCBs 13000 339 5 to 2,540 42 199 189 to 246 6 161 <67 to 247 8PAHs 3831 69 to 73,300 42 628 442 to 1145 8 26,013 <0.67 to 38,000 7Cl’d pesti-cides 33000 20 3.5 to 51.8 24 105 88.4 to 159 6 0

Dioxins, Furans, Planar CBs

CA tolerance level=133pg/g† pg/g pg/gCB/PCDD/

PCDF TEQ†† 8.27 1.70 to 17.5 4

* Dry tissue weight. To convert original data expressed as wet weights, assume 12% (oysters), 15% (mussels) and 16% (clams) dry weight.

† CA tolerance level (133 pg/g): Health Canada tolerance level for seafood consumption for 2,3,7,8-TCDD (133 pg/g DW = 20 pg/g WW; assume 15% solids).

†† Toxic Equivalency Concentrations for planar chlorinated biphenyls (CBs), dibenzo-dioxins (PCDD) and dibenzo-furans(PCDF) are based onn standardized factors for determining additive relative toxicities of these compounds that share a similar mode of toxicity.

TABLE 2.7Toxic contaminant concentrations in bivalve shellfish tissue from sites in Coastal New Hampshire and in Maine sites in Portsmouth Harbor: 1985-1997.

Concentrations of organic contami-nants in mussels in Table 2.7 are com-pared to FDA Action Levels for fish andshellfish. The organic contaminants ana-lyzed that have Action Levels includedPCBs, dieldrin, aldrin, chlordane, hep-tachlor, heptachlor epoxide, DDT andmethyl mercury. Action Levels for totalPCB and DDx are presented in Table 2.7.All reported organic concentrations areless than, and in most cases, far belowthe action levels. However, the PCB con-centrations at the Dry Docks on SeaveyIsland and at sites in the upper Pis-cataqua River were only 5-8 times lowerthan the action limit of 13 µg/g.

The effects of contaminants on thephysiology of mussels has also beenassessed in a few studies. Gilfillan et al.(1985) found effects of contaminants onmussel physiology assays were morerelated to metals than to aliphatic or aro-matic hydrocarbons in Portsmouth Har-bor. They found Cd, Zn, Ag, Cr and Cuaffected activities of glucose-6-phosphatedehydrogenase, aspartate amino trans-ferase and scope for growth assays inmussels for some sites some of the time,although effects were not consistentlymeasured at any specific site. Jones et al.(1998), reported that copper and zincconcentrations in mussel tissue from Lit-tle Harbor and Shapleigh Island in 1991and 1992 exceeded critical body residuelevels, or the lowest concentrations atwhich observed toxicity effects havebeen observed. Gulfwatch andPortsmouth Naval Shipyard studies havealso reported extensive information onmussel growth and condition index, aswell as limited information on scope forgrowth of mussels. The condition indexdata for indigenous and deployed mus-sels in New Hampshire indicate musselgrowth and physiological condition arewithin normal ranges, although some-what lower than other areas of the Gulfof Maine (Chase et al., 1997; 1998; Joneset al., 1998). The scope for growth meas-ured in deployed (caged) mussels inCutts Cove was the only indication ofstress in deployed mussels in PortsmouthHarbor (NCCOSC, 1997).

A recent report from the USEPA (Met-calf and Eddy, 1995) reviewed publishedcontaminant databases and determinedbackground concentrations for contami-nants in shellfish in New England andthe North Atlantic continental shelf areas.Comparison of the lowest observed con-taminant concentrations in New Hamp-shire mussels to the regional backgroundconcentrations showed concentrations ofcadmium, PAHs, PCBs and DDx wereclose to background concentrations atsome New Hampshire sites (Table 2.8).Other contaminants, especially arsenic,mercury and zinc, were present only atmuch higher concentrations, suggestingubiquitous, regional sources of thesecontaminants.

Other studies have reported contami-nant concentrations in different shellfishspecies. These data are summarized inTables 2.7 and 2.9, and in greater detailin Appendix H. Isaza (1989) also ana-lyzed clams (Mya arenaria), lobsters andsediments. Nelson (1986) analyzed oys-ters from four sites in the Great Bay Estu-ary for chromium and lead. Oysters wereanalyzed for a range of contaminants aspart of the Portsmouth Naval Shipyardstudy (Johnston et al., 1994; NCCOSC,1997). Langan and Jones (1995c) ana-lyzed oyster (Crassostrea virginica) sam-ples from Great Bay, and comparedresults to previous studies. Comparisonof concentrations to USFDA Action Lev-els shows only lead in the clams fromHilton State Park at Dover Point exceed-ed the 11.5 µg/g Action Level. Relativelyhigh concentrations of mercury in oys-ters, PAHs in clams and chromium inclams were also observed (Table 2.7).The lowest DDx concentrations in oys-ters were relatively close to backgroundconcentrations while concentrations ofcadmium, chromium and PCBs were rel-atively high. Conversely, most contami-nants that could be compared showedrelatively low, and sometime lower, con-centrations compared to backgroundconcentrations.

Numerous studies have reported con-taminant concentrations in differenttypes of lobster tissue (Table 2.9). PCB

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concentrations in adult muscle and vis-cera tissue from Pierces Island inPortsmouth Harbor were in excess of the13 µg/g action limit. These data are fromthe initial study that served as the basisfor the lobster consumption advisory inNew Hampshire (Isaza et al., 1989). Rel-atively high concentrations of cadmiumand mercury were also observed in somedifferent lobster tissue from various areasaround Portsmouth Harbor.

Plant tissue levels of contaminantshave also been reported (Table 2.10). Aspart of the Portsmouth Naval Shipyardstudy (Johnston et al., 1994), contami-nants were measured in eelgrass (Zosteramarina), fucoid algae (Ascophyllumnodosum) and winter flounder (Pleu-ronectes americanus). In the winterflounder samples, contaminant concen-trations were well below FDA action lev-els. Concentrations of metals in eelgrassand fucoid algae showed elevated con-centrations of some metals, and appar-ently different accumulation rates forsome metals compared to mussels. Fishtissue from Peverly Ponds and Bass Pondat Pease AFB indicated all organic con-taminants were below detection limits,except for DDT compounds (NHDES,unpublished data).

Sowles et al. (1996) reported heavymetal and organic contaminant concen-trations in small mouth bass and white

suckers from the Salmon Falls River. Mer-cury concentrations were similar to con-centrations found in fish from lakes andponds that prompted a fish consumptionadvisory in Maine. PCB and DDT con-centrations also exceeded some humanhealth threshold levels, and both metaland organic contaminant concentrationsat some sites were near concentrationsconsidered harmful to wildlife.

There have been numerous studies oncontaminant concentrations and impactson birds in the Gulf of Maine region. Inaddition, NHDES contracted in 1997 witha private company to provide wildliferescue and rehabilitation in response tooil spills.

In general, only rare occurrences oftissue contaminant concentrations ex-ceeded USFDA Action Levels. However,USFDA Action Levels may be higher thanconcentrations that can cause humanand wildlife health problems. The rela-tively high concentrations for severaltrace metals and toxic organic contami-nants are a concern, especially whenthey are consistently well above regionalbackground concentrations. The cumula-tive effects of elevated concentrations ofmultiple contaminants are not well char-acterized, but certainly present a prob-lem for the living resources and humansthat inhabit the coastal areas of NewHampshire. Recent studies on the role of

PAHs PCBs DDT andAs Cd Cr Cu Hg Ni Pb Zn total total metabolites

Background concentrations*(Gulf of Maine) 0.23 0.20 0.30 1.40 0.01 0.30 0.60 3.70 0.04 0.01 0.01

Lowest concentrations†

(New Hampshire) 5.10 0.10 1.50 5.50 0.13 1.30 2.10 80 0.07 0.01 0.01

USFDA Action Levels 25 87 6.7 533 11.5 13 33

* Background concentrations of contaminants in shellfish in New England and North Atlantic continental shelf area. From Metcalf and Eddy (1995).

† Lowest (background) concentrations of contaminants in shellfish in New Hampshire/Portsmouth Harbor.

Published background concentrations in New England waters (Metcalf and Eddy, 1995) andobserved lowest concentrations for contaminants in blue mussels from coastal New Hampshireand Portsmouth Harbor.

TABLE 2.8

many of the same contaminants asendocrine disruptors, especially duringcritical early life stages of biota, is causefor concern for very low contaminantconcentrations. Continued assessmentsof contaminants in biota, like theGulfwatch program, are important toolsfor assessing potential risks and deter-mining trends in contaminant distribu-tion and fate. More studies of biological

effects would be useful to determine theoverall toxicity of contaminants in theenvironment in the more contaminatedestuarine areas. The detection of con-taminants in New Hampshire shellfishthat are close to background concentra-tions suggests that sites where thesesame contaminants are present at elevat-ed concentrations may indicate localizedsources.

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Lobster Homarus americanus Winter flounder Pleuronectes americanus

USFDA Tissue Concentration # of Tissue Concentration # of Contaminant Action Level Average* Range samples Average Range samples

Trace metals µg/g µg/g µg/g µg/g µg/g

Ag 1.0 0.25 to 3.01 24 0.3 0.008 to 0.66 4As 13 4.35 to 19.7 24 4.4 2.10 to 6.41 4Cd 25 4.7 0 to 15.4 27 0.1 0.01 to 0.16 4Cr 87 0.4 0.12 to 1.6 28 0.4 0.23 to 0.73 4Cu 112.3 15.3 to 332 25 10.3 0.27 to 22 4Hg 6.7 0.6 <0.14 to 2.39 26 0.15 0.10 to 0.21 3methyl Hg 6.7 1 0.07 to 4.61 11 0.15 0.05 to 0.25 2Ni 533 0.67 0.41 to 1.81 27 0.49 0.18 to 0.65 4Pb 11.5 0.2 0.04 to 0.41 28 0.2 0.06 to 0.37 4Zn 95.3 58.5 to 147 28 64.6 16.4 to 114 4

Toxic organics ng/g ng/g ng/g ng/g ng/g

PCBs 13000 1561 11.3 to 66,400 27 281 51.5 to 938 4PAHs 588 47.2 to 87,600 24 479 17.2 to 531 4Cl’d pesticides 33000 269 2.01 to 791 28 97 6.61 to 192 4

* Lobster tissue includes samples of tail, claw, hepatopancreas, viscera, cooked meat, cooked tomalley, for adults and juvenile animals.

Trace Zostera marina Spartina Spartina Ascophyllum metal leaves roots alterniflora patens nodosum

Ag 0.68 0.66 0.22 0.14 0.49As 1.3 4.5 1.2 1.2 15.2Cd 1.25 0.53 0.07 0.10 0.55Cr 1.7 9.2 2.0 2.3 0.73Cu 15.5 16.9 2.1 2.8 16.9Hg 0.02 0.05 0.01 0.02 0.04Ni 1.82 3.09 0.69 0.98 1.83Pb 2.4 10.9 0.97 1.8 2.3Zn 72 57 31 27 78

*From NCCOSC, 1997.

Trace metal contaminant concentrations (µg/g dry weight) in marine plant tissue at sites inPortsmouth Harbor and Great Bay Estuary. Data from NCCOSC, 1997.

TABLE 2.10

TABLE 2.9 Toxic contaminant concentrations (dry weight) in lobsters and winter flounder tissue from sites in New Hampshire, Portsmouth Harbor and the Isles of Shoals: 1985-1997.

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Eutrophication of estuarine and coastalwaters resulting from excess nutrient

input from anthropogenic sources hasemerged as a significant problem formany coastal areas. The two most impor-tant nutrients in terms of pollution arenitrogen and phosphorus, since they aremost commonly the limiting nutrients inaquatic ecosystems, though carbon, silicaand trace metals such as copper and ironalso play a role in primary productivity.In marine and estuarine waters, nitrogenis generally believed to be the primarylimiting nutrient, though phosphorus hasbeen identified as the limiting factor insome systems. In addition to the concen-trations of nitrogen and phosphorus, theN:P ratio may also be important for somespecies of algae.

The biological effects of nutrientenrichment can range from subtle toextreme. Species shifts in phytoplanktoncommunities can result in unfavorableconditions for estuarine biota, particular-ly for filter feeders such as bivalve mol-luscs. Massive blooms of phytoplanktoncan reduce water clarity, shade sub-merged aquatic vegetation (SAV), andreduce water column oxygen concentra-tion due to nighttime plant respirationand oxygen consumption. Blooms ofnuisance macroalgae can replace moredesirable forms of vegetation and createhypoxic or anoxic conditions that canimpact fish and invertebrates. Conditionsresulting from nutrient enrichment canaffect recreational activities such as fish-ing, boating and swimming as eutrophicsystems can be most unappealing forthese activities. Nutrient enrichment isalso suspected to be a factor in bloomsof harmful, toxin-producing algae incoastal and offshore waters. Finally,sources of biodegradable organic nutri-ents can be a direct cause of hypoxia andanoxia as heterotrophic bacteria can rap-idly consume dissolved oxygen as theydecompose organic substrates.

Assessing the trophic status or thedegree of nutrient enrichment of anywater body necessitates the measure-ment of a suite of parameters, since no

single measurement can clearly depicttrophic status (Kelly, 1991). In addition,the geometry (depth, width, length) andflushing characteristics or residence timeof water masses are important factors indetermining the susceptibility of anywater body to eutrophication (Kelly,1997). Measurements of dissolved nitro-gen and phosphorus (inorganic andorganic), turbidity or suspended solids,particulate organic matter, chlorophyll a(as a measure of phytoplankton primaryproductivity), dissolved oxygen, salinityand temperature are useful parametersfor assessing eutrophication. Other indi-cations of eutrophication involve meas-urements of changes in biota over time,such as areal coverage, distribution andcondition of seagrass and macroalgalhabitats, as well as species shifts inmicroorganism and macroalgal popula-tions. Nutrient monitoring programs havebeen conducted both historically (1973-1981) and more recently (1988-1996) inthe Great Bay Estuary by UNHresearchers, and as part of the SeabrookStation Environmental Studies in Hamp-ton Harbor by Normandeau Associates,Inc. Additionally, nutrient concentrationshave been included in studies of non-point source pollution in the Great BayEstuary (Jones and Langan 1993a; 1994a,b, c; 1995a, b, c; 1996a, b, c), and as partof a project assessing contamination ofgroundwater and surface waters by on-site sewage disposal (septic) systems inSeabrook and Hampton, NH (Jones etal., 1995, 1996). The monitoring andresearch studies are discussed here rele-vant to nitrogen, and to a lesser extentphosphorus, concentrations in NewHampshire estuaries.

2.4.1 NUTRIENT CONDITIONS IN NEW HAMPSHIRE’S ESTUARIES

The issue of nutrient overenrichment hasbeen addressed in the Great Bay Estuarythrough monitoring programs datingback to the early 1970s as well as morerecently in targeted studies of point andnonpoint nutrient inputs. Some of thedata includes measures of organic nitro-

2.4

INORGANIC AND ORGANIC

NUTRIENTS

gen and phosphorus, however, the mosttemporally and spatially expansive datasets include inorganic forms of nitrogen(NH4, NO2

+ NO3-) and phosphorus (PO4),

forms which are most readily availablefor use by primary producers.

The Great Bay Monitoring Programsupported by the GBNERR has includedmeasurement of inorganic nitrogen andphosphorus concentrations at three sitesin the Great Bay Estuary (Langan andJones, 2000). Sites in the tidal portion ofthe Squamscott River and at Furber Strait(junction of Little Bay and Great Bay)have been sampled at high and low tidesince 1988, while a site in the LampreyRiver has been sampled since 1992.Though spatially somewhat limited,these data provide an excellent databasefrom which short term changes in nutri-ent concentration can be detected. Inaddition, a substantial database generat-ed between 1973-1981, which includesdata from the Furber Strait/Adams Pointsite, allows for longer term trend analy-sis. The state shellfish program recentlybegan monitoring shellfish growingwaters for nutrients and other parame-ters, in addition to fecal indicator bacte-ria (Langan et al., 1999a).

Though concentrations differ betweenstations, the seasonal patterns are similar.Highest concentrations of inorganicnitrogen occur late fall through earlyspring, while the lowest concentrationsoccur in late spring through early fall.The seasonal pattern for PO4 is some-what similar, though following an initialdrop during spring phytoplanktonblooms, phosphate concentration oftenrebounds in summer. The timing of thespring phytoplankton bloom can varyconsiderably, depending on annualweather conditions, therefore the drop inN and P concentration can occur fromlate March to mid-May. At the FurberStrait site, maximum dissolved inorganicnitrogen (DIN=NH4 + NO3 + NO2) can beas high as 20 µM in winter months, whileminimum concentrations are generally <1 µM at times in the spring and summer.Annual mean DIN at this site rangedfrom 7-11 µM from 1988 to 1996, with aneight-year mean of 8.8 µM. Interannual

variation has been considerable and nolong-term trend in concentration from1988-1996 has been observed.Orthophosphate at Furber Strait hasranged seasonally from <0.10 µM to 1.5µM with the annual mean ranging from0.70 µM to 1.0 µM. The eight year meanis approximately 0.85 µM. Though attimes the N:P ratio can range from ashigh 40:1 to as low as 1:1, the long termmean N:P ratio at this site is ≈ 10.6:1,indicating possible nitrogen limitationwhen compared to the Redfield ratio of16:1. High tide concentrations of nitro-gen at this site are slightly higher than atlow tide, though this difference is incon-sistent and statistically not significant.Orthophosphate concentrations are simi-lar at high and low tides.

At the Squamscott River site (Chap-man’s Landing), nitrogen concentrationsare much higher than at Furber Strait.DIN concentrations at this site can reach40 µM during the winter and are general-ly <5 µM in spring and summer. Therapid drop in nutrient concentration inspring measured at Furber Strait is not asdramatic in the Squamscott River station,as spring turbidity, resulting from springwinds and freshwater runoff, often limitsphytoplankton production. Therefore,nitrogen concentrations do not reachminimum concentrations until summer.The annual mean DIN from 1988 to 1996at this site is ≈ 20 µM. DIN concentrationsare generally higher in low tide samples,indicating an upstream riverine source ofnitrogen in the Squamscott River. As wasthe case with the site at Furber Strait,there is considerable interannual variationin DIN concentration, though significantdifferences between years and trends inconcentrations have not been evident inthe eight year period. Orthophosphateconcentrations have ranged from <0.3 µMto nearly 2 µM, with the overall mean of≈ 1.25 µM. Though the N:P ratio can varywidely during the year, the overall eight-year N:P ratio is approximately 11:1, indi-cating some degree of nitrogen limitationlike that at Furber Strait.

Nitrogen concentrations measured atthe Lamprey River sample site are slight-ly higher than at Furber Strait, and lower

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than the Squamscott River. Concentra-tions of DIN can range from <1 µM to 30µM, with annual means from 1992-1996ranging from 10-14 µM. Orthophosphateis lower at this site than at the two otherlong term monitoring station, with amean concentration of ≈ 0.6 µM. N andP concentrations at this site vary widelyduring the year, however, the mean ratiois ≈20:1.

Two separate field programs conduct-ed concurrently from 1993 through 1995(Jones et al. 1997) included measure-ments of nitrogen and phosphorus insamples taken on a transect beginning atthe head of tide in the Oyster River, run-ning south through Little Bay into GreatBay and terminating near the Newfieldsboat launch on the Squamscott River(Figure 2.29). Samples were takenmonthly from a subset of stations withincreased frequency at all stations duringspring, summer and fall. Mean DIN con-centration was highest at the station locat-ed at the Durham WWTP outfall in theOyster River, and the influence of thetreatment plant outfall was observed inthe increased DIN concentration (18.8µM) just downstream during low orfalling tide. Otherwise, the highest con-centration of DIN was measured at themost upstream site in the Squamscott

River (25 µM), with decreasing concen-trations (5-8 µM) through Great Bay intoLittle Bay. At the head of tide in the Oys-ter River, mean DIN was ≈ 13 µM, whileat the mouth of the river, mean DIN was10 µM. A short distance from the rivermouth into Little Bay, mean DIN concen-tration (≈ 6 µM) was similar to FurberStrait and mid-Great Bay. Orthophos-phate concentrations exhibited a similarpattern, with upstream stations as well asstations downstream of the DurhamWWTF having the highest concentrations.Annual mean N:P ratios ranged from 7:1to 11:1, indicating nitrogen limitation.

A three year project designed to assessthe effect of storm events on concentra-tions of a suite of contaminants in thetributaries to Great Bay provided anexcellent database for assessing spatialdistribution of nutrient concentrations inthe freshwater and tidal portions of thetributaries (Jones and Langan, 1994a,1995a, 1996a). In addition to the inorgan-ic forms of nitrogen and phosphorus,particulate nitrogen was measured in yeartwo of the study, and dissolved organicnitrogen was measured in years two andthree. Sampling was conducted at thesame sites used in Figures 2.6 and 2.7during dry periods (no precipitation forfive days prior to sampling) and during

13.7 13.3

18.8

12.6

7.3 7.8

10.0

6.4 6.2

7.86.9

7.68.5

13.9

16.7

25.2

Oyster River Little Bay Great Bay Squamscott River

Dissolved Inorganic Nitrogen (µM)

Dissolved inorganic nitrogen (DIN) concentrations at sites along a transect from the Oyster FIGURE 2.29River through Little and Great Bays to Newfields on the Squamscott River.

the first low tide occurring within 24 hrsof a rainfall event of 0.5” or more. In yearone, eight dry and eight storm eventswere sampled, while in years two andthree, four storms were sampled on twoconsecutive days following storms. Inaddition to the tributaries, years one andtwo included stations in Hampton Harborand the lower Piscataqua River. Thoughconsistent effects of rainfall events onnutrient concentrations were not found,the dataset provides an excellent recordof the spatial distribution of nutrient con-centrations and a means of evaluatingnutrient loading from point and nonpointsources. The highest nutrient concentra-tions were consistently found in thefreshwater and tidal portions of theCocheco and Salmon Falls rivers. Relativeto other sites, nutrient concentrationswere also elevated in the freshwater por-tions of the Oyster River and in the tidalportion of the Squamscott River. Nutrientconcentrations were consistently low inHampton Harbor and the PiscataquaRiver. Relative to the forms of nitrogen,particulate nitrogen was generally a smallfraction of the total, and exceeded 10% ofthe total nitrogen only during phyto-plankton blooms at some sites. Dissolvedorganic nitrogen (DON) concentrationsoften exceeded DIN concentrations,however, DON represented a smallerfraction of the total at sites with the high-est combined nitrogen concentrations.

Nonpoint source pollution assess-ments in the Oyster and SquamscottRivers (Jones and Langan 1994a,c;1995a,c; 1996a) included measurement ofinorganic nutrients at sites along the tidalmainstem of the two rivers, sites in thefreshwater portions of the rivers, smallstreams entering both portions of therivers, and adjacent to suspected pollu-tion sources such as developments andagricultural sites. In the Oyster River, thehighest concentrations of dissolved nitro-gen and phosphate were found in thevicinity of the Durham WWTF outfall andimmediately above the tidewater dam inthe Mill Pond. The greatest influence onoverall nitrogen concentration, however,was from the treatment plant. A nitrogenand phosphorus plume was detectable at

upstream stations all the way to the headof tide during flood tides, and as fardownstream as Johnson Creek and some-times Bunker Creek during ebb tides. Thehigh nutrient concentration from theWWTF plume made it difficult to deter-mine the relative strength of other tidalsources. Samples taken upstream of theMill Pond, in both the main stem of theriver and in smaller tributaries such asCollege Brook and Pettee Brook fre-quently had higher nitrogen concentra-tions than the water coming over thedam. A similar situation was found inBeards Creek which has a smallimpoundment before reaching the tidalportion of the river. The data indicatesthat impoundments can potentiallyremove nitrogen either via uptake byphytoplankton and macrophytic aquaticvegetation, or by biogeochemical pro-cesses such as denitrification or burial.

In the Squamscott River, a trend ofdecreasing nutrient concentration wasidentified from the head of tide in down-town Exeter to the mouth of the River insouthwestern Great Bay (Jones and Lan-gan, 1995c). Freshwater concentrationsof nutrients were lower than tidal con-centrations, indicating that the primarysources of nutrients were downstream ofthe tidal dam and may include the ExeterWWTF, runoff from the urban portion ofExeter, overflow from a CSO impound-ment, dairy farms such as the Stuart Farmin Stratham and possibly the Rocking-ham Country Club golf course. Elevatednitrogen concentrations at the mouths ofsome marsh creeks whose drainage wasundeveloped indicated that marshes maybe exporting nitrogen.

Water column nutrient concentrationsin the lower estuary were measured aspart of the Ecological Risk AssessmentStudy for the Portsmouth Shipyard (Lan-gan, 1994). This project included an ini-tial set of replicate samples taken at 21stations in the Piscataqua River, followedby monthly samples taken at low tide fora two year period at a subset of six sta-tions. Nitrogen concentrations followed aseasonal pattern similar to the upperestuary, with the highest concentrationsoccurring in late fall through early spring,

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and the lowest concentrations (0-1 µM)measured from late spring through fall.Annual mean DIN for the six stations onthe harbor area ranged from ≈ 7-10 µM.The highest concentrations of NH4 andNO3 were measured in Cutts Cove, whichreceives ebb tide waters from North MillPond, and at the Sarah Long Bridge,close to the Kittery, ME shore, just down-stream from the Kittery WWTF.Orthophosphate concentrations weresimilar at all stations with the annualmeans ranging from 0.6 to 0.8 µM andindividual measurements ranging from0.2 to 1.2 µM.

The Portsmouth Shipyard Risk Assess-ment project also included three fixedstation tidal stage studies, four crosssec-tional transects and high and low tidelongitudinal transects conducted in July1993. Data from transects and fixed sta-tion studies in the lower river and at themouth of the Harbor indicated that nitro-gen concentrations were very low, andgenerally on the order of 0-1 µM regard-less of tidal stage. All lower estuary sam-ples had low PO4 concentrations as well,ranging from 0.3 to 0.6 µM. Nitrogenconcentrations were generally higher forthe Dover Point crosssectional transect,with NO2 + NO3 ranging from 1-5 µM,and NH4 concentrations ranging from 1-4 µM. The highest concentrations weremeasured in the upper Piscataqua Riverduring mid-ebb tide, indicating anupstream source of nitrogen. Longitudi-nal transects beginning at the mouth ofPortsmouth Harbor to the railroad bridgeon the Squamscott River were conductedat high and low tides on consecutivedays. NO2 +NO3 concentrations on thehigh tide transect ranged from 0-1 µMfrom the harbor mouth to Dover Pointand from 1-2 µM from Dover Point to theSquamscott River. For the low tide tran-sect, NO2 +NO3 concentrations were sim-ilar to those measured at high tide in thelower estuary, and with the exception ofsamples taken in the upper PiscataquaRiver and at the mouth of the SquamscottRiver, were slightly lower (0-1.5 µM)through Little and Great Bay. Ammoniumconcentrations were more variable forboth tidal longitudinal transects, ranging

from 0-5 µM. The lowest concentrationswere measured in the lower PiscataquaRiver and upper Great Bay at both tides,while the highest concentrations weremeasured at low tide in the upper Pis-cataqua and Squamscott rivers. The lon-gitudinal transect data indicates possiblesources of nitrogen from these two gen-eral (upstream) sources. Orthophosphateconcentrations, though low throughout,increased from the harbor mouth to theupper estuary at both tides, with concen-trations ranging from 0.3 to 0.8 µM.

A study of the sanitary quality of theshellfish growing waters in Little Harbor(Jones and Langan 1995c) includedmeasurement of nutrient concentrationsat sites in the vicinity of the Wentworthby the Sea golf course. Samples weretaken in the spring following fertilizerapplication and during a period of wetweather. Mean DIN concentrations atthree sites ranged from 6.16 µM to 10.2µM while mean PO4 concentrationsranged from 0.32 to 0.49 µM.

Based on the studies reviewed for thisdocument, some general statements canbe made regarding temporal and spatialpatterns of nitrogen and phosphorusconcentrations in the Great Bay Estuary.Throughout the estuary, the highestnutrient concentrations occur in late fallthrough early spring and the lowest con-centrations occur in late spring throughearly fall. This pattern is more welldefined for NO2 + NO3 than for NH4 andPO4. Spatially, the highest nitrogen con-centrations generally occur near theheads of tide, due either to freshwaterinfluences (Cocheco, Salmon Falls, Oys-ter Rivers) or to the location of municipalWWTF outfalls near the heads of tide(Oyster River, Exeter/Squamscott River,Salmon Falls River). Spatially, phosphateconcentrations are low in most of thefreshwater portions of the tributaries,highest in the upstream portions of thetidal rivers, and lower through GreatBay, Little Bay and down to the harbormouth. There is an inverse relationshipof salinity with nitrogen concentration,with the lowest concentrations occurringin the lower Piscataqua and Little Bay. Bycomparison with nutrient concentrations

in other estuaries in the Northeast U.S.,the Great Bay Estuary probably fallssomewhere in the middle of the field.

By comparison to the Great Bay Estu-ary, very little data on nutrient conditionsexists for the Hampton/Seabrook Estu-ary. A long term dataset has been estab-lished by Normandeau Associates (NAI,1996), however, only one station outsidethe Harbor has been monitored and thedata do not accurately represent condi-tions in the estuary. As part of a two yearstudy of the potential for groundwaterand surface water contamination fromseptic systems (Jones et al., 1995; 1996),nutrients were measured in groundwaterand surface water at sites in Seabrookand Hampton. At eleven sites inSeabrook, groundwater wells were sam-pled in and around the effluent disposalareas (EDA) of residential homes. Sur-face waters down gradient of the EDAs,which were either fresh or brackishstreams, marsh creeks or the Harboritself, were also sampled. DIN concentra-tion in the wells ranged from 0.15 to 36mg/L, while the annual mean DIN con-centration in surface waters ranged from0.06 mg/L in the mouth of the Harbor to2 mg/L in some of the small freshwatercreeks. There was a decreasing nitrogenconcentration with increasing salinity forthe surface water samples. Based on thenitrogen concentrations and the directionof flow determined in the hydrologicalstudies, it appears that nitrogen is trans-ported from EDA to surface water, how-ever the resulting low nitrogenconcentrations in the harbor and theabsence of any signs of potentialeutrophication (low dissolved oxygen,algal mats, extreme phytoplanktonblooms, etc.) indicate that there is littleobservable impact to the estuary.Though phosphate was detected in highconcentrations in and around the EDAs,it did not appear to be as readily trans-ported in the groundwater to surfacewaters. PO4 concentration ranged from0.01 to 8.9 mg/L in the EDA and from0.01 mg/L to 0.06 mg/L in surface waters.A follow-up study in 1996-97 showednutrient concentrations in the same sur-face waters were not significantly differ-

ent from previous years, even thoughseptic systems were being disconnectedthroughout Seabrook (Jones, 1997).

2.4.2 TRENDS IN NUTRIENTCONCENTRATIONS

Assessing long term trends in nutrientconcentrations requires consistent sam-pling and analytic protocol over anextended period of time. Though someof the studies described above were con-ducted for two or three consecutiveyears, normal variation in water columnconcentrations makes it difficult to detecttrends. Nutrient data generated for theGreat Bay NERR Monitoring program,which has included sampling and analy-sis for eight years at two of the three sta-tions indicates that there is considerableinterannual variation in nutrient concen-trations. However, statistical analysis ofthe eight years of data (ANOVA) does notindicate any significant differences ineither nitrogen of phosphate concentra-tions between years nor are any trends ofincreasing or decreasing concentrationsevident. The data collected as part of theGreat Bay Field Program (Loder andGilbert 1977; 1980; Loder et al., 1983;Daley et al., 1979; Norall, et al., 1982)included low tide sampling and analysisat stations that included a site at FurberStrait, identical to the 1988-1996 site sam-pled in the GBNERR monitoring pro-gram. Analytical methods for the earlierand more recent datasets were not iden-tical, however, they were sufficiently sim-ilar to enable comparisons of nutrientconcentrations. When all compatible(depth sampled) data for the earlier andmore recent datasets were compared,mean NH4 concentration was slightlyhigher in 88-96 dataset (3.51 µM) than inthe 1973-1981 dataset (2.57 µM). Con-versely, mean NO2 +NO3 concentrationwas slightly lower from 1988-1996 (5.25µM) than 1973-1981 (5.60 µM). Mean dis-solved inorganic nitrogen (NH4 + NO2

+NO3) at the Furber Strait site is thereforeslightly higher from 1988-96 (8.76 µM)than from 1973-1981 (8.17 µM). Thedatasets were compared statisticallyusing both parametric (t-test) and non-parametric methods and no significant

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difference in DIN concentration wasfound. Seasonal patterns were also ana-lyzed. There was considerable variationbetween years for samples taken duringa particular month, therefore monthlymeans for the earlier and recent datasetswere used for the purpose of compari-son. The seasonal patterns for NH4, NO2

+NO3 and DIN for the two datasets wereremarkably similar to the data for DINpresented in Figure 2.30. As was the casewhen all data were compared, monthlymean NH4 concentrations were slightlyhigher in the more recent dataset, andNO2 +NO3 were slightly lower.

Two additional studies conducted in1976-1977 (Daley and Mathieson, 1979;Loder et al., 1979) allow an evaluation ofchanges in riverine nitrogen concentra-tions over a nearly 20-year period.Hourly water samples were collectedthroughout full tidal cycles in July andAugust in 1976 and 1977 (Daley andMathieson, 1979) immediately seawardof the tidal dams and at sites downstreamof the tidal dams and analyzed for NO2

+NO3. The mean concentrations werecompared to July and August means forequivalent sample sites collected for var-ious studies from 1993-1996. These dataare presented in Figure 2.31 and 2.32.

Increased concentrations over the nearly20 year period are observed in the fresh-water sites in the Cocheco and SalmonFalls rivers (Figure 2.31) while nitrite-nitrate concentrations are lower in thefreshwater and estuarine portions of theOyster and Bellamy Rivers (Figure 3.32).Similar concentrations for the two peri-ods were observed in the Lamprey andSquamscott rivers.

Monthly data were collected and ana-lyzed for nitrate-nitrite at the terminalfreshwater areas of the Great Bay tribu-taries from February 1976 through June1978 as part of study on nutrient fluxprocesses in the estuarine system (Loderet al., 1979). Sample means were calcu-lated and compared to data collected forseveral studies at identical sites from1993-1996 (Jones and Langan, 1996a;Langan and Jones, 1996; Jones et al.,1997). The results are similar to the July-August data comparisons. Nitrate-nitriteconcentrations at all sites with the excep-tion of the freshwater areas of theCocheco and Salmon Falls rivers areeither similar to or lower in the morerecent dataset, indicating improvementsor no change in all tributaries except theSalmon Falls and Cocheco rivers, whereconcentrations have increased. Statistical

Jan Feb Mar Apr May June July Aug Sept Oct Nov Dec

DIN 1974-81

DIN 1988-96

DIN µM

0

2

4

6

8

10

12

14

16

18

Monthly mean dissolved inorganic nitrogen at Adams Point in Great Bay for the years FIGURE 2.301973-81 and 1988-96.

FIGURE 2.32 Nitrate/nitrite concentration trends in saltwater portions of tributaries to the Great Bay Estuary.

analysis (t-tests as well as nonparmetrictests) indicate significantly higher con-centrations of nitrate-nitrite in the fresh-water portions of the Cocheco andSalmon Falls rivers, significantly lowerconcentrations in the freshwater andestuarine portions of the Oyster and Bel-lamy rivers, and no significant differ-ences for the Lamprey and Squamscottrivers between data from the mid-1970s

and the mid-1990s. Based on the data reviewed for this

report, it is possible to make some gen-eral statements regarding trends in nutri-ent concentrations in the Great BayEstuary. Despite a dramatic increase inpopulation from 1970 to 1990 (and aslower increase since 1990) throughoutthe Great Bay watershed, and thereforean expected increase in nitrogen loading,

94

Squamscott Lamprey Oyster Bellamy Cocheco Salmon Falls

1976-781993-96

9.68.1

6.1 6.5

20.2

7.5

11.2

5.8

17.8

14.4

9.9

11.4

Total N concentration (mg/l)

FIGURE 2.31 Nitrate/nitrite concentration trends in freshwater portions of tributaries to the Great Bay Estuary.

Lamprey Oyster Bellamy Cocheco Salmon Falls

1976-781993-96

Total N concentration (mg/l)

6.1 5.7

17.6

13.0

8.5

6.3

17.1

29.4

14.7

27.5

95

recent data indicate that current nutrientconcentrations (annual means, seasonalpatterns, minimum and maximum con-centrations) in most areas of the estuary,including the tidal tributaries are similarto or lower than that which wasobserved in the 1970s. The exceptionsare the Cocheco and Salmon Falls rivers,and in particular the freshwater portionsof those rivers, where concentrationshave increased in recent years. One pos-sible explanation is that the expectedincreased loading from increased popu-lation has been offset by improvementsin municipal wastewater treatment inmost areas.

2.4.3. RELATIONSHIP TO WATER QUALITY STANDARDS

Though water quality criteria for estuar-ine waters have been established forsome parameters such as metals, fecalindicator bacteria and dissolved oxygen,examples of concentration limits fornitrogen are rare. The Town of Fal-mouth, Massachusetts (1994) adopted athree tiered nitrogen concentration

approach intended to limit future nitro-gen inputs. Total nitrogen concentrationsof 0.32, 0.5 and 0.75 mg/L total N wereestablished as critical concentrations forwater bodies of varying usage and classi-fications. Though the Great Bay Estuaryhas different characteristics than waterbodies in the Town of Falmouth, it isuseful to compare nitrogen concentra-tions in Great Bay to the standards estab-lished for Falmouth. Total nitrogen datafor Great Bay locations were obtainedfrom several studies described above,including the three year study of thetributaries (Jones and Langan (1994a,1995a and 1996a) and data from a non-point source assessment extending fromOyster River through Squamscott River(Jones et al., 1997). Results are presentedin Figure 2.33. None of the mean con-centrations of total N, including thefreshwater portions of the Cocheco andSalmon Falls rivers, exceed the 0.75 mg/Lupper limit set for Falmouth. Sitesexceeding the Falmouth medium con-centration criteria (0.5 mg/L) includeboth the freshwater and tidal portions of

FW FW MiddleGreatBay

LowerPiscat-aqua

SW SW FW SW FW SW FW SWFW

M

FALMOUTH

H

L

SW

Squam-scott

Lamprey Oyster Bellamy Cocheco Salmon FallsExeter

M=0.50 mg/l

H=0.74 mg/l

L=0.32 mg/l

Comparison of total nitrogen concentrations for Great Bay Estuary and its freshwater and FIGURE 2.33 estuarine tributaries with Falmouth, MA water quality benchmarks.

the Salmon Falls and Cocheco rivers.Sites exceeding the Falmouth low limit(0.32 mg/L) include the freshwater andtidal sites in the Exeter/ SquamscottRiver, the tidal sites in the Lamprey andOyster rivers, and the freshwater site inthe Bellamy River. Sites in the freshwaterportion of the Lamprey River (0.30mg/L), Little Bay/Bellamy River (0.29mg/L) mid-Great Bay (0.27 mg/L) andthe Piscataqua River (0.23 mg/L) are alllower than the Falmouth lower limit of0.32 mg/L. The Great Bay Estuary couldgenerally be characterized as havinghigher turbidity, greater flushing andgreater depth than the water bodies sur-rounding Falmouth, therefore it is likelythat it is less sensitive to higher nitrogenconcentrations (Nixon and Pilson 1983).

2.4.4 POLLUTION SOURCES ANDNITROGEN LOADING ESTIMATES

In general, sources of nutrients to estuar-ies include natural sources such as water-shed sediments, organic debris (leavesand other vegetation) and groundwater,as well as point and nonpoint sources ofanthropogenic origin. Anthropogenicpoint sources include industrial andmunicipal wastewater while nonpointsources include urban and agriculturalrunoff, stormwater conduits, on-sitewastewater treatment (septic) systems,lawn fertilizers and atmospheric deposi-tion of nitrogenous compounds thatresult from burning of fossil fuels.

Loading estimates to water bodies arefrequently based on modeling exercises.Values for nitrogen contribution, eithermeasured from previous studies or esti-mated from literature values, can beassigned to all types of land use andcover (urban, forested, wetland, activeagriculture, lawns, impervious surfaces),population and method of waste dispos-al in a watershed. Coupled with meteor-ological (rainfall) and other physical data(soil type, river discharge) the land useand land cover data can be used to esti-mate annual loading of nutrients. TheNOAA Status and Trends Branch (NOAA,1989), estimated annual loading to theGreat Bay Estuary of 636 tons of nitrogenand 204 tons of phosphorus. Of these

totals, it was estimated that point sourcesare responsible for 242 tons of nitrogenand 161 tons of phosphorus, while non-point sources are responsible for 394tons of nitrogen and 43 tons of phos-phorus. The method used to make theseestimates is unclear, but it is assumedthat it was some type of modeling studybased on satellite derived (GIS at1:24,000) land use/land cover data andpredetermined values for nitrogen contri-bution. Another NOAA publication fromthe Strategic Assessment Branch (NOAA,1994) estimated the total nitrogen inputfrom point sources to be 317 tons peryear. This estimate was based on effluentvolume monitoring and typical waste-water concentrations of nitrogen.

Sources in Great Bay include municipalwastewater treatment plants, septic sys-tems, urban and suburban (lawn fertilizer)runoff, and atmospheric deposition.Though agriculture is often cited as amajor source of nutrients to estuaries, thisis probably not the case in Great Bay.Though some farms may input nutrientsat specific locations (i.e., Aikman DairyFarm on the Salmon Falls River and StuartFarm on the Squamscott River) there isvery little active agriculture in the water-shed, and therefore little possibility forsystem-wide loading of nutrients fromagricultural sources. The models that usecurrent GIS data to estimate nutrient load-ing may tend to overestimate the contri-bution of agriculture, since some of theland identified as active agriculture hasnot been farmed for many years. Addi-tionally, some of the larger farms adjacentto the estuary (those mentioned above)have recently adopted, with the assistanceof the NH Coastal Program and the Nat-ural Resource Conservation Service(NRCS), best management practices toreduce contamination from animal wastesand fertilizer application.

The numerous studies on nutrientconcentrations described in the earliersection of this report, in addition to stud-ies on streamflow and river discharge(Pappas, 1996), atmospheric deposition(Mosher, 1995), and on effluent qualityfrom local sewage treatment plants (Mit-nik, 1994) have made it possible to esti-

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mate loading to the Great Bay Estuaryfrom actual measured data. There is alsosome data available on urban stormwater(Jones, 1998b; Jones and Langan, 1996a),however most of the urban developmentin the NH Seacoast is located at theheads of tide, and most stormwater isdiverted to the freshwater portions of thetributaries and would therefore beincluded in the fluvial (riverine) loadingestimates. For the purposes of this report,this exercise was limited to nitrogen,since it has been identified as the limitingnutrient in most estuaries, includingGreat Bay.

Fluvial (riverine) loading, whichincludes both natural and anthropogenicsources, was calculated by using mean

monthly concentrations of total nitrogen(DON + DIN + PN) measured over athree year period in the tributaries toGreat Bay (Jones and Langan 1994a,1995a, 1996a) and river discharge meas-ured and calculated by Pappas (1996).These data are presented in Figure 2.34.Nitrogen loading estimated for tributariesto the tidal portions of the Oyster River(Jones and Langan 1993a, 1994c) andSquamscott River (Jones and Langan1995c) were small (on the order of < 1ton annually from all tributaries) by com-parison to the main stem of each riverand to WWTFs, and were therefore notused in the calculations. Throughout theyear, the months with the greatest loadingare understandably the months of great-

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Bellamy

Oyster

Exeter

Lamprey

Cocheco

Salmon Falls

Tons N/year

0

5

10

15

20

25

30

35

Annual loading of nitrogen from fluvial (riverine) sources to the Great Bay Estuary. FIGURE 2.34

Bellamy River Oyster River

Exeter/Squamscott River

Lamprey River

Salmon Falls River

Cocheco River

30%

2%

16%

17%

32%

3%

Nitrogen loading to the Great Bay Estuary from fluvial (riverine) sources. FIGURE 2.35

est river discharge. Peaks in loadingoccur in March and April and in Novem-ber and December (Figure 2.34). Riverinenitrogen contribution to the Great BayEstuary is greatest from the Cocheco andSalmon Falls rivers, followed by theExeter and Lamprey rivers, with thesmallest amount from the Oyster and Bel-lamy rivers (Figure 2.35). Nitrogen load-ing in the summer, or during dryerperiods of the year, is greatest in theSalmon Falls River, followed by theCocheco and Lamprey rivers. On anannual basis each river contributes thefollowing in tons of N and % of total:Cocheco 143 (32%); Salmon Falls 134(30%); Lamprey 78 (17%); Exeter 74 (30%);Oyster 12 (3%) and Bellamy 9 (2%) for atotal of 450 tons of nitrogen per year.

Point source contribution was calculat-ed using total nitrogen concentrationsmeasured in wastewater effluent from theMilton, Berwick, South Berwick, Somer-sworth, Rollinsford and Dover WWTFs(Mitnik 1994) and the Durham WWTF(Jones and Langan 1994c) and averageeffluent volume reported by the treat-ment plants. For those plants where nitro-gen concentration was not measured, amean nitrogen concentration calculated

from the treatment plants with measureddata were applied. Point source loadingfrom municipal WWTFs is presented inFigure 2.36. The largest nitrogen input, indescending order, is from thePortsmouth, Rochester, Dover, ExeterBerwick and Kittery WWTFs. Eventhough the volume from the Berwickplant is relatively small, the nitrogen con-tribution is high due to high nitrogen(especially ammonium) concentration inthe effluent. From these data, it is esti-mated that the total point source (WWTF)contribution of nitrogen to the Great BayEstuary is 296 ton of nitrogen per year.This figure is greater than the 1990 NOAAestimate of 242 tons and slightly less thanthe 1994 NOAA estimate of 317 tons,although it does not include loading fromsix industrial NPDES dischargers to theEstuary (Table 2.1).

In order to calculate point and non-point nitrogen loading, nitrogen contri-bution from treatment plants upstream ofthe tidal dams (Farmington andRochester on the Cocheco River; Milton,Berwick, Somersworth and Rollinsfordon the Salmon Falls River) was subtract-ed from the annual fluvial loads calculat-ed for the rivers. This results in a total of

98

Tons per year

0.86

27.99

9.52

0.67 1.51

30.29

62.69

4.32

13.82

8.63

1.04

32.81

2.07

22.28

78.23

Sout

h Be

rwic

k

Milt

on

Berw

ick

Som

mer

swor

thRo

llins

ford

Dov

er

Roch

este

r F

arm

ingt

on

Dur

ham

New

mar

ket

New

field

s

Exet

er

New

ingt

on

Kitt

ery

Port

smou

th

FIGURE 2.36 Nitrogen input to the Great Bay Estuary from municipal wastewater treatment plants.

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296 tons/year from municipal pointsources, and 345 tons per year from flu-vial sources (nonpoint sources).

Atmospheric deposition was calculat-ed by Mosher (1996) for the Great Baywatershed. Since nitrogen loading fromland deposition would be included in thefluvial source estimates, only direct dep-osition (to the water surface) was con-sidered. The estimate for directdeposition was 77 tons/yr, which in addi-tion to the point and nonpoint loading,totals 718 tons per year of nitrogen. Thepercentage contribution from the threesources is 48% from nonpoint sources,41% from point sources and 11% fromdirect atmospheric deposition (Figure2.37). The 718 tons per year is slightlygreater than the 640 tons per year esti-mated by the NOAA Strategic AssessmentBranch in 1990. In a smaller study con-ducted as part of a nonpoint sourcesassessment of the Oyster River in 1994,remarkably similar results with regard tothe ratio of point and nonpoint contribu-tions were obtained. Data generated bythat study (Jones and Langan 1994c) esti-mated that 42% of the nitrogen loadingto the Oyster River was from the DurhamWWTF which contributed approximately11 tons of total N per year.

It should be noted here that some lib-erties were taken in assignment of nitro-gen inputs as either point or nonpoint. Itis unlikely that the entire nutrient loadfrom sewage treatment plants locatedwell upstream of the estuary (Farming-ton, Rochester, Milton, etc) is delivered tothe estuary. Therefore, attributing all ofthe nitrogen from these plants to pointsources may result in an overestimate ofpoint source contribution, and an under-estimate of nonpoint source contribution.The total would not differ, however, sincenonpoint was determined by subtractingthe nitrogen contribution of upstreamWWTFs from the total fluvial load. Onanother note, including the entire annualnitrogen contribution of the PortsmouthWWTF to estuarine loading may overesti-mate actual nitrogen loading to the estu-ary. The subsurface diffuser on thedischarge pipe ensures rapid dilution,and the location of the outfall (near the

mouth of the harbor), plus the character-istics and residence time of the receivingwaters makes it unlikely that all or mostof the nitrogen is transported upstream tothe estuary, and that possibly up to 50%of the nitrogen is carried out of the estu-ary into the Gulf of Maine.

Although nonpoint (riverine) andatmospheric sources exceed point sourceinputs of nitrogen, these sources includenatural as well as anthropogenic sources.Point sources (WWTFs) on the otherhand, are almost entirely of anthro-pogenic origin. Therefore, loading fromthese sources becomes much moreimportant when planning for futuredevelopment and if it becomes necessaryto consider nutrient reduction strategies.

As was the case with nutrient concen-trations, nitrogen loading limits have notbeen established for the Great Bay Estu-ary. The State of Maine DEP (Mitnik andValleau, 1996; Mitnik, 1994) has conduct-ed a WASP modeling and Total Maxi-mum Daily Limit study (TDML) on theSalmon Falls River, and found that thereare nitrogen and phosphorus impacts(excessive phytoplankton and depressedoxygen) in the freshwater impound-ments, and phytoplankton impacts(depressed oxygen) to a small portion ofthe tidal section of the river during dryperiods in summer. This study will bediscussed in the section detailing impactsof eutrophication.

The Buzzards Bay NEP establishedloading limits (expressed in g/m2 ofwater surface area/year) for anthro-pogenic nitrogen to the estuary. Similarto the Falmouth, MA concentration limits,

TotalPoint Source

Total NPS

Direct ATDeposition

41%

11%

48%

Sources of nitrogen loading to the Great Bay Estuary. FIGURE 2.37

a tiered approach to nitrogen loadingwas established depending on the depthand flushing characteristics of sections orsubunits (subwatersheds of BuzzardsBay). Loading per unit area to the GreatBay Estuary was determined by using theestimates previously described (718tons), and dividing by the surface area ofthe estuary (10,900 acres). The resultswere compared to the loading limitestablished for deep, SA (class A waters)in Buzzards Bay with a flushing time of>5 days. This would represent an aver-age estimate for the Great Bay Estuary,since the depth range is very broad, andflushing time can range from hours toweeks, depending on the exact locationin the estuary. Loading to Great Bay(Lower Little Bay and all of Great Bay)was also calculated, using the area(approximately 5,000 acres) and loadingfrom the Exeter, Lamprey, and Oysterrivers (fluvial) and WWTFs in Exeter,Newfields, Newmarket and Durham.Direct deposition of nitrogen fromatmospheric sources in proportion to thesurface area was also considered. TheBuzzards Bay limit for shallow class Awaters with a flushing time > 5 days wasused for comparison. Results of thesecalculations and comparison to loading

limits established for Buzzards Bay arepresented in Figure 2.38. Loading to theentire Great Bay Estuary was calculatedto be 14.5 g/m2/year and loading toLower Little Bay and Great Bay was cal-culated to be 10.4 g/m2/year. Both thesefigures are below the 20 g/m2/year fordeep water and 15 g/m2/year for shal-low water established for Buzzards Bay.

It must be stated, however, that theseestimates are a first attempt to assess thenitrogen loading to the Great Bay Estuaryfrom actual water quality data. Sinceloading was based on mean nitrogenconcentrations, which can be highly vari-able in riverine waters as well as inwastewater, there is a degree of uncer-tainty for those areas where sample sizewas small or where the effluent concen-tration was estimated. The contribution ofnitrogen from groundwater sourcesdirectly to the estuary is unknown.Though soils in the Great Bay Estuary dif-fer from those estuaries that have signifi-cant input of nitrogen from groundwater(Buttermilk Bay and Waquoit Bay, MA), itmay be possible that additional nitrogenloading occurs through direct groundwa-ter input to the estuary. Since groundwa-ter loading is not considered, this couldresult in an underestimate of the total

100

Great Bay Estuaryand Tributaries

Buzzards Bay WQC(Deep - SA)

Great BayOnly

Buzzards Bay WQC(Shallow - SA)

14.74

20.00

10.58

15.00

FIGURE 2.38 Comparison of nitrogen loading in the Great Bay Estuary with water quality criteria standardsestablished for Buzzards Bay, MA.

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loading. There is also a degree of uncer-tainty in the validity of Great Bay to Buz-zards Bay comparisons due to differencesin hydrographic condition, watershedgeology and topography. Mean tidalheight at the mouth of the Great BayEstuary is approximately 2.7 meters, con-siderably greater than in Buzzards Bay(1.7 meters), and there is also greatermean water depth in some sections of theGreat Bay Estuary. Though these differ-ences would suggest that the Great BayEstuary can handle a greater amount ofnitrogen loading than Buzzards Bay, theuncertainties mentioned, in addition tothe absence of a nitrogen budget for theGreat Bay Estuary that includes accurateestimates of rates of nitrogen processes(uptake, burial, remineralization, denitrifi-cation), would make a definitive state-ment of that nature premature. Also, thelimitations for Buzzards Bay were foranthropogenic nitrogen, whereas allsources of nitrogen were considered forthe Great Bay analyses.

Nutrient loading has not been estimat-ed for the Hampton/Seabrook Estuary.Sources of nutrients include groundwatercontaminated by septic systems, theHampton WWTF located on Tide MillCreek, some small amount of active agri-culture, and urban and suburbanstormwater runoff. Hampton Harbor isquite unique in that it receives an 88%exchange of water on each tide (twicedaily). Therefore, the residence time ofthe water in the estuary is on the orderof hours, even for the upstream areas.This residence time is probably too shortto support intense phytoplanktonblooms, and indeed there is no evidenceof these occurring (Jones, 1997). Thenitrogen concentrations measured in theestuary and outside the harbor mouth(NAI, 1996) indicate that despite theprobability that the estuary receivesnitrogen input from point (WWTF) andnonpoint sources (septics, stormwater,etc.), there appears to be sufficient dilu-tion to reduce concentrations of nitrogento low levels. The absence of other indi-cators of nutrient overenrichment such aspoor water clarity, low dissolved oxygen,dense macroalgal mats and proliferation

of opportunistic algal species supportsthe finding that excess nutrient input isnot a problem in Hampton Harbor. Addi-tionally, the town of Seabrook hasrecently finished the process of linkingall the residences to a centralized munic-ipal sewage system. The outfall for theWWTF is located in the Atlantic Ocean,therefore the possibility of any impactfrom contaminated groundwater (fromseptic systems) will be permanentlyremoved.

2.4.5. DOCUMENTED IMPACTS ONWATER CHEMISTRY AND NATURAL RESOURCES

The biological effects of nutrient enrich-ment can range from subtle to extreme.Species shifts in phytoplankton commu-nities can result in unfavorable condi-tions for estuarine biota, particularly forfilter feeders such as bivalve molluscs.Massive blooms of phytoplankton canreduce water clarity, shade submergedaquatic vegetation (SAV), and reducewater column oxygen concentration inthe dark via respiration. Blooms of nui-sance macroalgae can replace moredesirable forms of vegetation and createhypoxic or anoxic conditions that canimpact fish and invertebrates. Conditionsresulting from nutrient enrichment canaffect recreational activities such as fish-ing, boating and swimming as eutrophicsystems can be most unappealing forthese activities.

2.4.5.1 Dissolved Oxygen

One of the principal concerns associat-ed with nutrient overenrichment andeutrophication is reduction in dissolvedoxygen (D.O.) due to elevated aerobicmetabolism. Low D.O. (hypoxia) or thetotal absence of D.O. (anoxia) canseverely impact aerobic marine andestuarine organisms and threaten thevitality of aquatic ecosystems. Dissolvedoxygen is an important indicator andone of a suite of ecological endpointsfor eutrophication.

Dissolved oxygen has been measuredin association with many monitoring andresearch programs. In the Great BayEstuary, dissolved oxygen can vary at all

times of the year depending on temper-ature of the water. Colder, fresher water,has a great capacity for dissolved oxy-gen. Therefore, in winter, dissolved oxy-gen will be higher in the upper reachesof the estuary than in the more oceaniclower portions of the estuary. As thewaters warm and salinity increases insummer in the upper estuary, dissolvedoxygen will be lower than in the coolerlower estuary. Thus, the annual variationis expected to be greater in the uppertidal reaches of the estuary. Dissolvedoxygen concentration is also affected bythe depth of the water, the amount ofmixing, residence time of the water, tidalstage and at certain times of the year, thetime of day.

Though the absolute value of dis-solved oxygen (measured in mg/l) isimportant, the degree or percent of oxy-gen saturation is a more accurate meas-ure of the potential for biological effects.In general adverse biological effects arenot evident unless dissolved oxygendrops below 5 mg/L for an extendedperiod of time. The State of New Hamp-

shire has established 75% saturation asthe water quality standard for D.O. fornot less than 16 hours per day and notless than 6 mg/l at any time except asnaturally occurs. It is suspected thatsome shallow upper estuarine systemsmay drop below 75% saturation in theabsence of eutrophication relatedimpacts (Kelly, 1995).

Even though sites in mid-Great Baycan have dissolved oxygen ranging from6 to 15 mg/liter throughout the year, per-cent oxygen saturation is usuallybetween 90-110% (Figure 2.39) (Langanand Jones 1996). Lower estuary measure-ments vary similarly and are almostalways near 100% saturation (Langan,1994). Water column measurements indi-cate that there is little stratification andthat dissolved oxygen is similar in valueand percent saturation throughout thewater column. In the tributaries to GreatBay, dissolved oxygen can vary from 5mg/l during early morning low tides insummer to 16 mg/l in winter. Percent sat-uration in the Squamscott River, forexample, can range during the year from

102

130

120

110

100

90

80

70

% O2 Saturation

1988 1989 1990 1991 1992 1993 1994 1995 1996

FIGURE 2.39 Monthly measurements (high and low tide average) of percent oxygen saturation at the AdamsPoint station from July, 1988 to June, 1996.

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70% to 120%, depending on the time ofday, tidal condition, and time of year(Figure 2.40).

In a three year project designed toassess the effect of stormwater runoff oncontaminants in tributaries to Great Bay,measurements of dissolved oxygen weremade in the freshwater portions of thetributaries and in the mouths of the tidalportions (Jones and Langan, 1994a,1995a, 1996a). Data from this study indi-cates that dissolved oxygen in the fresh-water portions of the rivers can get quitelow, particularly at times of low flow.Freshwater measurements of D.O. oftenfailed to meet the New Hampshire waterquality criteria (WQC) of 75% saturation.Saturation in the tidal sites was generally70% to 100% with few NH WQC viola-tions. Though the water quality problemsin the freshwater portions of the rivermay be related to eutrophication, it islikely that the summer low flow condi-tions result in stagnant conditions in theimpoundments above the dams and thatthe sediment oxygen demand as well asrespiration exceeds the oxygen repletion

rates in water with poor rate ofexchange. This condition is alsoacknowledged in the New HampshireWQC, which includes a statement thatWQC be met, “...except as naturallyoccurs”. The low dissolved oxygen con-ditions measured in point samples in theExeter River was verified in the summerof 1995 using a continuous datalogger. InAugust, 1995, dissolved oxygen rangedfrom 3 to 4 mg/L and 35% to 60% satu-ration. It should be noted however, thatthe summer of 1995 set a record for lowrainfall and that the section of the riverwhere the instrument was deployed wascompletely stagnant for weeks. Autumnstorms, which produced increased flow,improved oxygen saturation to 80% bylate October.

A study conducted by the Maine DEP(Mitnik and Valleau, 1996; Mitnik, 1994)measured dissolved oxygen at a series ofstations in the freshwater and tidal por-tions of the Salmon Falls Rivers. Thesestudies were conducted during the sum-mers of 1993 and 1995, both of whichwere extremely dry. Depressed oxygen

130

120

110

100

90

80

70

%O2 Saturation

1988 1989 1990 1991 1992 1993 1994 1995 1996

FIGURE 2.40Monthly measurements (high and low tide average) of percent oxygen saturation at the Squam-scott River station from July, 1988 to June, 1996.

conditions were detected at several sta-tions in the freshwater portion of theriver and near the bottom of a deep site(Hamilton House) in the upper tidal por-tion of the river. In 1959, average D.O.was less than 6 mg/l at sites along thelower seven miles of the freshwater por-tion of the river, with minimum values of0 mg/l, and much higher levels in tidaland upstream freshwater sections of theriver (NHWPC, 1960). In the the MaineDEP studies, the remaining stations inthe tidal portion of the Salmon Falls Riverand in the Piscataqua River ranged from80%-100% saturation at all depths. At thetidal site near Hamilton House in SouthBerwick, ME, the surface D.O. was usu-ally near 100% saturation while the 5meter depth D.O. was frequently below50% saturation and was actually anoxicon one occasion in August. The low dis-solved oxygen in the Salmon Falls Riverwas attributed to eutrophication (intenseplankton blooms) in the freshwater por-tion of the river, sediment oxygendemand (in deeper water) and stagna-tion caused by the series of impound-ments on the river and extremely lowflow conditions. The eutrophic condi-tions were attributed to excessive phos-phorus from the four sewage treatmentplants discharging to the river. An exper-imental phosphorus limitation period in1995 resulted in significant reduction inphytoplankton in the impoundments.Based on recommendations from theMaine DEP study, upgrades of WWTFs inBerwick, ME, South Berwick, ME,Rollinsford, NH Milton, NH and Somer-sworth, NH are required to limit phos-phorus discharges to the Salmon FallsRiver over the next few years.

Based on the existing data, it can besummarized that, in general, the GreatBay Estuary does not exhibit low dis-solved oxygen conditions in the tidalwaters. Even the shallow upper tidalreaches of the rivers exceed 5 mg/L inworst case scenarios (early morning lowtides in mid to late summer), with anoccasional measurement between 4.5and 5 mg/L. It should be noted, howev-er, that at some of these sites the period-ic drops in oxygen at low tide in early

morning may be a natural phenomena,particularly in very shallow water nearmarshes (Stanley and Nixon, 1992;Stokesbury et al., 1996). The warm tem-peratures and rich organic sedimentsresult in high benthic respiration ratesand could potentially draw down watercolumn oxygen. The duration and spatialdistribution of hypoxic effects are ofgreater importance with respect to bio-logical effects than the instantaneousmeasurement of the level of dissolvedoxygen (Stokesbury et al., 1996). Contin-uous attainment of the WQC for dis-solved oxygen set by Maine DEP (85%saturation) and New Hampshire (75%)may be unrealistic and not achievable incertain water bodies, even in undis-turbed estuarine systems. Perhaps atiered approach similar to the Falmouth,MA nitrogen concentration standardswould be appropriate.

A review of available data does indi-cate, however, that the freshwater por-tions of some of the rivers (Salmon Falls,Exeter) can experience low dissolvedoxygen episodes, and often for periods ofup to several weeks during very low flowconditions in the summer. For the SalmonFalls River, the low dissolved oxygen canbe attributed to excess nutrient inputfrom WWTFs exacerbated by stagnant,impounded waters (Mitnik and Valleau,1996; Mitnik 1994; Jones and Langan1994a, 1995a, 1996a). It is unknown ifthere are present biological impacts asso-ciated with the low dissolved oxygenconditions in the freshwater impound-ments. Historically, the existence ofstretches of downstream, freshwater por-tions of the river being “devoid of fishdue to lack of oxygen” was noted in thereport by NHWPC (1960).

As is the case with nutrient data, thereis considerably less data on dissolvedoxygen in the Hampton/Seabrook Estu-ary than in Great Bay. As part of theSeabrook Station Environmental StudiesProgram, Normandeau Associates, Inc.has maintained a long term record of sur-face and bottom dissolved oxygen at asite outside the Harbor, but none in theestuary itself. The study of the potentialof groundwater and surface water

104

105

impacts from on-site sewage disposalsystems described in an earlier section(Jones et al., 1996) was extended toinclude measurements in the summer of1996 of dissolved oxygen in a numberof small freshwater streams, marshcreeks, larger tributaries and in the Har-bor itself (Jones, 1997). Out of a total of139 samples taken in tidal streams andsmall marsh creeks from July, 1996 toJune, 1997, seven D.O. measurementsbelow 5 mg/l were recorded, all at lowtide during the summer and early fallearly in the day in small tidal creeks. Allof the forty-seven measurements in thelarger tributaries and in the Harbor itselfwere > 5 mg/l and generally greaterthan 75% saturation. Although thedataset is limited, it indicates that thereare no low dissolved oxygen conditionsthat could result in biological impact inthe Hampton/Seabrook Estuary.

2.4.5.2 Phytoplankton Blooms

The timing and intensity of phytoplank-ton blooms (as measured by water col-umn chlorophyll) varies spatially in theGreat Bay Estuary. Blooms in Great Bayand Little Bay generally occur in springand fall, with variation between these

two seasons as to when peak concentra-tions occur. Summer concentrations aregenerally lower than these peaks due tograzing, but are higher than winter con-centrations. Peak concentrations atFurber Strait can reach as high as 20 µg/l(on one occasion in 1993 and one in1994) but are usually on the order of 5-10 µg/l. Figure 2.41 represents chloro-phyll concentrations averaged for highand low tides at the Furber Strait site.The average annual chlorophyll concen-trations have ranged from < 2µg/l to >3.5 µg/L with an eight year mean con-centration of 3.2 µg/l. Chlorophyll con-centrations in the lower estuary have asimilar seasonal pattern (Langan, 1994),with blooms occurring in spring and fall.However, the peak concentrations arelower than in Great Bay, rarely exceed-ing 3 µg/l. Continuous measurements ofchlorophyll were made on flood tide andebb tide cruises in July, 1992, from themouth of the harbor to the railroadbridge on the Squamscott River (Chad-wick et al., 1993). On the flood tide,chlorophyll concentrations ranged from1 to 1.5 µg/l from the harbor mouth toDover Point; 2.5 to 3 µg/l in the upperPiscataqua River; 2-3 µg/l in lower Little

25

20

15

10

5

0

Chlorophyll a (µg/L)

1988 1989 1990 1991 1992 1993 1994 1995 1996

FIGURE 2.41Monthly measurements (high and low tide average) of chlorophyll a at the Adams Point stationfrom July, 1988 to June, 1996.

Bay and 3-3.5 µg/l through upper LittleBay and Great Bay. Concentrations wereslightly higher in some areas during theebb tide cruise, however, the range of 1-3.5 µg/l was similar.

Peak concentrations in the tidal riversfollow a different pattern than areas inGreat Bay, Little Bay and the lower Pis-cataqua River. Rather than a distinctspring bloom, chlorophyll concentrationsgradually increase through the spring,and peak concentrations occur at somepoint from August through October. Inthe Squamscott River, peak concentra-tions for the period 1988 through 1996were ≈ 30 µg/l, however, the peak inAugust, 1994, was 80 µg/l. The laterblooms in the rivers are probably due tolight limitation (from higher turbidity) inthe spring.

Spinney Creek, a salt pond in Eliot,Maine, is susceptible to intense phyto-plankton blooms by nature of its limitedexchange of water (long residence time)with the Piscataqua River and elevatedtemperatures. The blooms can occur atany time from spring through fall and,the fall blooms are often the mostintense. In the fall of 1996, a bloom ofthe naked dinoflagellate Protocentrumspp. lasted for several weeks and causedmortalities in oysters (Ostrea edulis)being raised in the creek. The cause ofthe bloom was attributed to regenerationof nutrients from macrophyte decay andlittle to no water exchange.

Bloom conditions in the other tribu-taries are best illustrated by examiningdata collected as part of a three yearproject to assess the effect of stormwaterrunoff on contaminant concentrations(Jones and Langan, 1994a, 1995a, 1996a).Intense blooms were recorded for twoconsecutive days after a rainstorm thatfollowed an extended dry period in Sep-tember, 1995. Highest intensities wererecorded in the freshwater and tidal por-tions of the Salmon Falls and Cochecorivers, suggesting that there may be peri-odic intensive bloom conditions in thefreshwater and upper tidal reaches ofthese Rivers. These data are confirmedby Maine DEP studies in the Salmon FallsRiver (Mitnik and Valleau, 1996; Mitnik,

1994) where intense blooms wererecorded in the freshwater impound-ments and spilled over into the uppertidal portion of the river. Impacts to thetidal portion of the river were limited tolow D.O. in bottom waters in a deephole (6 m) adjacent to the HamiltonHouse. The low D.O. in the surfacewaters (fresh) was attributed to the res-piration from phytoplankton bloom(caused by excess phosphorus and nitro-gen from point sources), high water tem-peratures and long residence time of thewater in the impoundments due to verylow flow conditions, while the low bot-tom water D.O. was attributed to sedi-ment oxygen demand.

Chlorophyll data collected at FurberStrait from 1973 to 1981 was compared tothe 1988-1996 dataset. Means for the twoperiods were very similar: 3.4 µg/l for the1973-1981 period and 3.2 µg/l for the1988-1996 period. Seasonal patternswere also similar, as were minimum val-ues (0 µg/l). The maximum value for theearlier data was 14 µg/l, and 20 µg/l inthe more recent dataset. This comparisonindicates that there has been little or nochange on water column chlorophyllconcentration over the 22 year period atthis site.

Phytoplankton primary productivity, asmeasured by chlorophyll concentration,has been measured for many years out-side the Hampton/Seabrook Estuary (NAI,1996), however, it has been only recentlythat chlorophyll has been measured atsites within the estuary. Jones et al. (1997)measured chlorophyll concentrations in anumber of small freshwater streams,marsh creeks, larger tributaries and in theharbor itself beginning in July 1996. Peakchlorophyll concentrations in the summerwere approximately 3 µg/l in the largertidal rivers and in the Harbor, and up to28 µg/l in the small tidal creeks. Concen-trations at all sites dropped through thefall and winter. Additional samples havebeen collected as part of the New Hamp-shire Estuaries Program to provide animproved spatial and temporal represen-tation of the chlorophyll concentrations inHampton Harbor.

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2.4.5.3 Eutrophication

The Great Bay Estuary and other estuar-ine areas in New Hampshire had nocited incidences of eutrophic or hypoxicproblems prior to 1985 (Whitledge,1985). This report was a review ofeutrophic or hypoxic estuaries nation-wide, and more detailed New Hampshireinformation is provided below.

In addition to elevated nutrients,depressed dissolved oxygen conditionsand phytoplankton blooms, other poten-tial indicators of eutrophication includeproliferation of opportunistic (green)macroalgae, reduction in water clarity,and loss of eelgrass. There has beensome speculation that opportunisticmacroalgal populations have increasedin recent years (A. Mathieson, personalcommunication), however, this has notbeen substantiated with measured data.A project conducted during the summerof 1997 as part of the GBNERR monitor-ing program examined areal coverageand biomass of macroalgal species alongan intertidal gradient for which an excel-

lent baseline was established in 1973(Chock and Mathieson, 1979). Nochanges in species, biomass and percentcover were documented (Langan andJones, 1999).

Water clarity in the Great Bay Estuaryis most affected by resuspension of finegrained sediments. Resuspension of sed-iments can result from human activities,such as dredging and boating in shallowwater, however, natural causes, and inparticular wind driven waves are the pri-mary cause of resuspension (Anderson,1974, 1975). Suspended sediments willbe discussed in another section of thisreport, however it is useful to note herethat at the two long-term monitoring sitesin the Great Bay Estuary, suspended sed-iment concentration has decreased inrecent years, and the annual mean is sig-nificantly lower at Furber Strait in theyears 1993-1996 than from 1988 through1992 (Figure 2.42).

Relative to eelgrass, a decline in thelate 1980s in Great Bay attributed to thewasting disease, was followed by recov-ery in the 1990s. Areal coverage, density

50

40

30

20

10

0

Total suspended solids (mg/l)

1988 1989 1990 1991 1992 1993 1994 1995 1996

FIGURE 2.42Monthly measurements (high and low tide average) of suspended solids at the Adams Point sta-tion from July, 1988 to June, 1996.

and biomass now exceed the early1980s. Eelgrass has also been observedrecently in areas where it has beenabsent for many years. It appears thateelgrass populations in the Great BayEstuary are in good condition.

Based on the nutrient, dissolved oxy-gen and chlorophyll conditions, as wellas the other potential indicators, there isno indication of system-wide eutrophica-tion in the Great Bay Estuary, nor arethere any documented trends that wouldindicate increasing nutrient enrichment.The physical characteristics of the estu-ary, including tidal height, relative flush-ing, a vertically mixed water column andhigh turbidity, in addition to the suite ofparameters examined, would indicatethat eutrophication in Great Bay is not animminent problem. Though the dataindicate that nitrogen may be limiting,light is also an important limiting factordue to resuspension of sediments andvigorous vertical mixing. There are indi-cations, however, of potential problemsin the freshwater portions of some of thetidal rivers and in the upper tidal reach-es of the Salmon Falls and Cochecorivers. Though both point and nonpointsources may contribute to the problemsobserved there, low water flows anddams (impounded stagnant waters) con-tribute to water quality impacts. Thelocation of a large point source on theCocheco River (Rochester WWTF) andseveral smaller point sources (several

WWTFs) on the Salmon Falls River areno doubt responsible for a large portionof anthropogenic nitrogen loading tothese rivers. Though the potential forsystem-wide impacts from these rivers isremote, increasing the nitrogen load inthe upper tidal reaches of these riverscould impact water quality in longer tidalstretches of both rivers, and potentiallythe upper Piscataqua River as well. Resi-dence time is an important factor indetermining sensitivity to nutrientoverenrichment. For that reason, the tidalportions of the Lamprey and Squamscottrivers and areas in the southern portionsof Great Bay would be considered areassusceptible to nutrient overenrichmentsince flushing times (complete waterexchange) can be from two to threeweeks for these areas in dry conditions.Therefore potential water quality impactsshould be considered before this area issubjected to additional loading.

Based on the nutrient, chlorophylland dissolved oxygen data reviewed, inaddition to the lack of any indicators ofeutrophication, there is no reason tobelieve that nutrient overenrichment isan issue in Hampton Harbor. Additional-ly, the rate of water exchange and shortresidence time of the water in the harborwould make it difficult for eutrophicconditions to develop in the estuary.With Seabrook-wide hook up to the newWWTF, future conditions are expected tobe even better.

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Rochester Wastewater Treatment Facility discharge

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Three review articles chronicle andsynthesize most of the information

available concerning suspended sedi-ments and turbidity in the Great BayEstuary. The Bibliography of the Geolo-gy of the Continental Shelf, Coastline andEstuaries of New Hampshire and Adja-cent Regions (Ward and Pope, 1992) is acomprehensive report of all available lit-erature up to 1992 concerning the geolo-gy and sedimentology of the NewHampshire region. An annotated bibliog-raphy for sediment based studies isincluded. A synthesis of the relevantresearch concerning the sedimentology(including the bottom and the water col-umn) of Great Bay was presented byWard (1992) and Short (1992). The mostrecent and up to date synthesis ofresearch on suspended sediments andturbidity in the Great Bay Estuary is pre-sented in A Monitoring Plan for the GreatBay National Estuarine Research Reserve:Final Report for the Period 07/01/95through 06/30/96 (Langan and Jones,1996). The synthesis of relevant research,annotated bibliography of relevant stud-ies, and complete bibliography of knowninformation presented here is based onthese reports. Ward and Pope (1992)forms the basis of the complete bibliog-raphy up to 1992. The synthesis by Ward(1992) forms the framework for thereview of existing information for sus-pended sediments and turbidity in theGreat Bay Estuary. Where appropriate,segments of these reports are repeatedhere, as well as updated. Langan andJones (1996), along within other recentreports, are used to update the synthesisand bibliographies.

2.5.1 SURFICIAL SEDIMENTS AROUND GREAT BAY ESTUARY

The surficial sediments in the Great Bayarea have been strongly influenced byglacial advances and retreats during theQuaternary period (the last two or threemillion years of the Earth’s history). Dur-ing the last major glaciation (referred toas the Wisconsin), which began ~85,000years ago and was at a maximum

~18,000 years ago (Flint, 1971), the largeice sheets removed much of the overly-ing soils and eroded the underlyingbedrock (Chapman, 1974). Subsequently,extensive tills (unsorted sediments) andmarine sands, silts and clays weredeposited by the retreating glaciers (Del-core and Koteff, 1989). More recently,modern tidal flats, salt marshes andmuddy to cobble beaches have devel-oped adjacent to the estuary and its trib-utaries.

2.5.2 SHORELINE CHARACTERISTICS IN THE GREAT BAY ESTUARY

The intertidal shoreline of the Great BayEstuary probably arrived close to its pres-ent day position a few thousand yearsago when the rise of sea level sloweddown. Since that time the estuary hasbeen continuously modified by a slowsea level rise (presently about 1.5 mm/y,Hicks et al., 1983), wave effects, tidalaction, biological processes, ice impact,and humans. Wave impacts in Great BayEstuary are most important on the mud-flat areas that often front the rocky orgravel shorelines (especially in the manyembayments). Resuspension of fine-grained sediments from mudflats occursduring frequent wind events, increasingthe turbidity of the nearshore and theoverall estuary. These processes are dis-cussed in more detail below. However,the wave energy is usually low andimpact on the coarse-grained (gravel)beach sediments is probably small inmany places.

Although no quantitative assessmentof shore types has been done for theGreat Bay Estuary (with the exclusion ofthe tidal marshes), qualitative observa-tions based on aerial photographs andfield observations have been made. Suchstudies indicate that exposed bedrockshorelines fronted by shingle beaches,small pocket beaches composed of sandto cobble size sediments, eroding tillbluffs of little relief, muddy tidal flats,fringing marshes located on bedrock orcoarse sediment, and large marshlandsare all commonly found. Most frequent-

2.5

SUSPENDED SEDIMENTS

AND TURBIDITY

ly, the shoreline is exposed bedrockeither fronted by cobble beaches, fring-ing marsh, relatively wide tidal flats, orlarge marshes. Large tidal flats dominatethe intertidal and subtidal portions ofGreat and Little bays. Consequently, thesurface area of the bays changes dramat-ically from high to low tide.

2.5.3 SOURCES OF SEDIMENTS

The sources of sediments for the inter-tidal and subtidal portions of Great BayEstuary originate primarily from shoreerosion, runoff from the watershed viainflowing rivers, and biological produc-tivity. Erosion of the exposed bedrocksurrounding much of the Bay providesirregularly shaped cobbles that form nar-row shingle beaches. Some minor sandybeaches are located adjacent to erodingtill deposits (e.g. Fox Point). Due to therocky nature of the land surrounding theestuary and the relative thinness of thetill deposits, it is unlikely substantialamounts of fine-grained sediment arecontributed from shore erosion. Conse-quently, the source of new fine-grainedsediments and turbidity is likely fromfreshwater tributaries. The impact ofriverine inputs is most important follow-ing heavy rains which are more frequentin the spring. Jones and Langan (1996a)found the total suspended sediment con-centrations in all the tributaries enteringGreat Bay following rain events to behigher than concentrations during dryperiods, although the differences wereless than 5 mg/l and usually not statisti-cally significant. In addition, all of theassociated rivers are dammed, reducingthis potential source. The source of sus-pended sediments and turbidity on a dayto day basis is more likely due to windand tidal resuspension of the extensivesubtidal and intertidal mudflats.

2.5.4 SUSPENDED SEDIMENTS

Spatially, the lowest suspended sedimentconcentrations occur in the lower estu-ary, while the highest generally occur inthe upper estuary or within the tidal por-tions of the estuarine tributaries (Squam-scott, Lamprey, Oyster, Bellamy,Cocheco, Salmon Falls or upper Pis-

cataqua rivers). Ward (1994) measuredthe suspended sediment concentrationsin the lower estuary (Portsmouth Harbor)and near the mid-estuary (Dover Point)over a number of tidal cycles in July,1992. The concentrations were low andvaried little across the channel and withdepth in Portsmouth Harbor. The totalsuspended sediment concentrationsranged from 1.1 to 3.7 mg/l over a com-plete tidal cycle at the mouth of the Har-bor and from 1.5 to 5.9 mg/l at across-section near Seavey Island. Similar-ly, Shevenell (1974) found suspendedsediment concentrations were generallyless than 3 mg/l at a station in the mouthof the Piscataqua River in 1972-1973,except during winter when concentra-tions exceeded 6 mg/l. According toShevenell (1974), the main sources ofparticulate matter in the coastal shelfwaters adjacent to the Piscataqua Riverwere biological productivity, resuspen-sion of bottom sediments and estuarinedischarge from the Piscataqua River.Shevenell (1974) also noted particulatematter concentrations fluctuated season-ally and spatially due to meteorologicaleffects (e.g., storms, high river dis-charges).

Total suspended sediment concentra-tions were higher in the mid-estuary,ranging from 2.4 to 12.7 mg/l over a tidalcycle at a cross-section at Dover Point inJuly, 1992 (Ward, 1994). The increase intotal suspended sediments in the mid-estuary over the concentrations meas-ured near the mouth reflects the impactof higher suspended sediment inputsfrom the upper estuary (e.g., Great Bay,upper Piscataqua River, tributaries).

The spatial pattern of the total sus-pended sediment concentrations fromthe mouth of the estuary in Portsmouthto the upper estuary is reflected in theresults of transects run in July, 1992(Ward, 1994). The concentrations meas-ured at ~high tide or early ebb rangedfrom 1.3 mg/l at the mouth to 17.7 mg/lat the entrance to the Squamscott River.Concentrations along the same transectrun at ~ low tide and during the earlyflood ranged from 2.4 mg/l to over 50mg/l at the Squamscott River.

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Temporally, the highest concentrationsoccur in spring and fall, while summerand winter have lower concentrations(data from Loder et al. 1983, in Short,1992). The total suspended sediment con-centration off Furber Strait in the GreatBay averaged 11 mg/l from 1976 to 1978,with the lowest values in fall and winter.Unpublished data from Ward during 1991to 1992 shows a similar pattern for FurberStrait. Short (1992) indicated the maxi-mum suspended sediment concentrationsoccurred in the 1970s, although the aver-ages are similar.

Langan and Jones (1996), focusing onthe upper estuary, found that the sus-pended sediment concentrations fromsummer, 1995 to summer, 1996 werehighest in the lower reaches of theSquamscott River (measured at Chap-mans Landing) ranging from 5.8 to 42.7mg/l and averaging 20.5 and 15.1 mg/l at

low and high tide, respectively. The sus-pended sediment concentrations atFurber Strait ranged from 3.3 to 22.8 mg/land averaged 9.8 and 7.5 mg/l at lowand high tide, respectively. These aver-ages are slightly lower than measured inthe mid to late 1970s and in 1991/1992.Langan and Jones (1996) found the sus-pended solids concentrations at sites atChapmans Landing and Furber Straitsdecreased from 1988 to 1996, significant-ly in some cases. Clear seasonal patternswere not apparent at these sites (Figures2.42 and 2.43).

Lower concentrations for the 1995-1996 period were measured in the Lam-prey River than in either the SquamscottRiver or at Furber Strait (Langan andJones, 1996). Suspended sediment con-centrations averaged 3.8 mg/l at bothhigh and low tide in the Lamprey at theTown Landing. The suspended sediment

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Total suspended solids (mg/l)

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FIGURE 2.43Monthly measurements (high and low tide average) of suspended solids at the Squamscott Riverstation from July, 1988 to June, 1996.

concentrations in the Oyster Riverappeared to be similar to values meas-ured for the Squamscott River (Jones andLangan, 1993a). Interestingly, there wereno distinct differences on a seasonalbases in the Oyster River, nor were thereconsistent spatial variations. The averageconcentration in Oyster River were high,with a low tide mean of nearly 35 to 40mg/l. However, this mean included sam-ples taken in shallow water stations inthe upper tidal reaches where local windresuspension and other processes biasedthe results. The overall changes withtime in the Great Bay Estuary need to beexamined further.

The periodic nature of the suspendedsediment load in the estuary has beendescribed by Anderson (1970) whodemonstrated large changes in concentra-tions over tidal cycles and over seasons.Suspended sediment concentrationsranged from ~2 to 18 mg/l in the channelat the entrance to the Bellamy River in Lit-tle Bay in response to tidal currents,resuspension events, spring discharge

and ice effects. Large increases in the sus-pended sediment load can occur overtidal flats due to small amplitude waves(Anderson, 1972, 1973), extreme watertemperatures caused by tidal flat expo-sure during summer months (Anderson,1979; 1980), desiccation of the tidal flat(Anderson and Howell, 1984), rainimpact (Shevenell, 1986; Shevenell andAnderson, 1985) and boat waves (Ander-son, 1974; 1975). Webster (1991) investi-gated bedload transport on a tidal flat inGreat Bay and found that the transportrates were related primarily to wind waveactivity, although tidal currents may haveenhanced movement. Webster (1991),also found that the benthic communityappeared to affect bedload transport bydisturbing the tidal flat surface (pelletmounds and feeding traces). Sedimentsresuspended along the shallow flatsmixes with the channel waters, resultingin higher turbidity in the estuary. Thus,sedimentary processes which occur alongthe shallow flanks of the estuary have alarge impact on the overall water quality.

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Adams Point in winter

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2.5.5 SEDIMENTATION PROCESSESON GREAT BAY TIDAL FLATS

Anderson (1983) summarized the physi-cal and biological processes influencingmuddy intertidal flats, emphasizing theGreat Bay. Anderson (1983) concludedthat the main physical factors were:effects of ice, waves, sediment dewater-ing, mud and water temperatures, andrain. Biological factors included growthof benthic diatoms, algal mats,macrovegetation, bioturbation, pellet for-mation, biodeposition and changes inmudflat microrelief. Ice effects dominatein winter and early spring with breakupcausing erosion. Wind resuspension wascommon much of the year. During sum-mer, biologic processes dominate anddeposition is more common. Storm activ-ity in fall as biologic processes slowcauses increased tidal flat erosion.

Wave action on the muddy intertidalflats causes erosion, resuspension, andsubsequent transportation of the sedi-ments. Tidal currents serve to distributethe sediments which are introduced viariverine sources, from bluff erosion, orfrom resuspension episodes on inter-tidal flats. In addition, strong tidal cur-rents limit the seaward expansion of thetidal flats.

Sedimentation processes on the shal-low tidal flats around the Great Bay arestrongly influenced by biologic process-es. Black (1980) found deposit feedersingest muddy sediments, creating fecalpellets that behave hydraulically likefine-sand grains. Estimated feeding rates,for example, of Macoma balthica indi-cate the surface sediments are turnedover 35 times per year (Black, 1980).Sickley (1989) demonstrated that tidal flaterosion was related to decreases inmicrobial populations and to the grazingactivity of epibenthic macroorganisms.Sickley (1989) also showed suspendedsediment concentrations to be related tobenthic algal populations, which tend tobind the sediment.

Because of the temperate climate ofthe estuary, ice plays an important role inshaping the geomorphic and sedimento-logic characteristics of the shoreline.

During most winters much of the shore-line and intertidal regions of the bay arecovered with ice. Ice tends to modify theshoreline by pushing sediments aboutand by forming gouges in the softer,muddy tidal flats. In winter during peri-ods of ice movement, large amounts ofsediment, clumps of marsh, and sea-weeds are transported and eventuallydeposited elsewhere in the Bay (Math-ieson et al., 1982; Hardwick-Witman,1986; 1985; Short et al., 1986). Thompson(1975) found that ice on a tidal flat nearAdams Point contained 0.58 to 27.2grams of sediment per liter of ice.According to Thompson (1975), up to 50cm of sediment was eroded from innerportions of the tidal flat, while up to 25cm was deposited along the outer por-tion. Overall, the ice impact appeared tobe erosional.

Suspended sediments have beenmeasured in the Hampton/SeabrookEstuary as part of the 1994 Sanitary Sur-vey (NHDHHS, 1994a), and was includ-ed in surface water sampling for studieson potential surface water contaminationfrom septic systems (Jones, 1997). Sam-ples have also been collected and ana-lyzed from sites in the estuary as part ofthe monitoring supported by the NHEP.Total suspended solid concentrations inthe Harbor are generally quite low, rang-ing from 1 to 6 mg/L, while in the small-er tidal creeks concentrations can beconsiderably higher, depending on tidalstage and wind speed and direction.

2.6.1 RADIONUCLIDES

The US EPA has published radiologicalsurveys of the Portsmouth Naval Ship-yard. Two of these documents have beenobtained (USEPA, 1979; 1991). For boththe 1977 and 1989 samples, materialsfrom sites around Seavey Island and theGreat Bay Estuary included sediments,sediment cores, biota and water. The1977 study also included samples of veg-etation and air samples. The results ofboth studies showed no evidence ofradioactivity released as a result of Navalnuclear propulsion plant operations,based on cobalt-60 analyses. Detectableradioactivity in the biota and the envi-ronment surrounding the shipyard wasattributed to naturally occurring isotopesor atmosphere-borne isotopes indicativeof past nuclear weapons testing.

Seabrook Station has an extensiveradiological monitoring program of themarine environment around SeabrookStation. The monitoring programincludes sampling and radiologicalanalysis of seawater, sediment, fish, lob-ster, mussels and algae in the area nearSeabrook Station and the offshore cool-ing system discharge area, as well ascontrol stations of similar environmentalmedia collected in Ipswich Bay, Massa-chusetts. Continuous air samples are alsocollected at eight locations and directradiation is measured at 42 locationsaround Seabrook Station. This is aug-mented by 16 additional direct radiationmonitoring locations along the immedi-ate Station fence line. All direct radiationmonitoring locations include the use ofsix separate passive detectors. In addi-tion, milk is collected from seven milkfarms around Seabrook Station.

The program began in 1984, morethan five years before Seabrook Stationbegan operation. No radionuclides attrib-utable to the operation of Seabrook Sta-tion have been detected. Naturallyoccurring radionuclides have been iden-tified by the program including K-40, Be-7, Th-232 and its daughter products.Cesium-137 was detected in milk in verysmall quantities as the result of fallout

from atmospheric nuclear weapons test-ing. The levels of radionuclides are con-sistent with those measured during thepreoperational phase of the monitoringprogram. All analytical results are sub-mitted to the U.S. Nuclear RegulatoryCommission in the Annual RadiologicalEnvironmental Monitoring Report.

2.6.2 BIOTOXINS

Paralytic shellfish poisoning (PSP) wasfirst recorded in 1972 in this portion ofthe Gulf of Maine (GOM). Alexandriumspp., blooms are probably transportedsouth to New Hampshire coastal watersfrom a source population near the mouthof the Kennebec/Androscoggin rivers inMaine (Franks and Anderson, 1992).Local conditions may have some effecton blooms even though occurrences inNH are typically associated with largeregional occurrences in ME & MA.

The NHDHHS, with support fromNHF&G, conducts weekly sampling ofmussels (Mytilus edulis) for PSP analysesat one site in Hampton Harbor. Since1983, blooms have occurred during latespring to late summer. During 1983-89,the average weekly PSP levels were peri-odically >44 µg PSP/100 g tissue (thedetection limit) & over the closure limit of80 µg PSP/100 g tissue (NAI, 1996). Redtide blooms were reported to occur on aregular basis in 1989 (NHDES, 1989a), butonly rarely since 1991 (NAI, 1996). PSPwas detected at >44 µg PSP/100 g tissuein 1991, 1993 & 1994, but only duringMay-early June. PSP was detected atincreasing concentrations on 3 consecu-tive occasions in May, 1995. Even thoughconcentrations were below the closurelimit, flats were closed because of thetrend and some ME flats had already beenclosed. In 1996, there were no closures(NHDHHS, unpublished data). Concentra-tions of PSP remained at <44 µg/100 gmussel tissue from 4/1/96 to 10/27/96 inHampton Harbor. Monitoring programs inboth Maine and Massachusetts provideuseful additional information. Little otherinformation is available to documentother harmful algal bloom events. 114

2.6

OTHER CONTAMINANTS OF POTENTIAL CONCERN

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2.6.3 ACID RAIN

The NHDES has a database for acid rainat NH lakes and ponds (NHDES, 1996c).The results show an increase in pH inprecipitation over the past 15 years from4.0 to 4.3, and a significant increase inalkalinity over the past 15 years in someponds. Even though most New Hamp-shire lakes showed no significant changein pH over the past 15 or 50 years, manylakes are still vulnerable to acid rain andhave pH values of <6.0. No data are col-lected for tidal waters.

Acid deposition is primarily a result ofemissions of nitrogen (NOx) and sulfur(SOx) oxides into the atmosphere. Mon-itoring of NOx has been conducted bythe NHDES Air Resource Division atManchester and Portsmouth since 1986,and SOx has been monitored at fourteenlocations since the mid-1970s (NHCRP,1997). Power generation produces 90%of SOx and 39% of NOx emissions inNH, while mobile sources produce 51%of the NOx. National Ambient Air Quali-ty Standards are 80 µg/m3 for SO2 and 53ppb for NO2. The annual mean concen-trations for these two gases havedecreased since 1990, from 10.63 to18.58 µg/m3 for SO2 and from 24 to 12ppb for NO2.

2.6.4 MARINE DEBRIS

Data on marine debris clean up effortssince 1992 have been summarized bySalem High School (SHS, 1996). Theinformation includes collection sites,numbers of debris items, type of debris,temporal trend analysis, and other dataanalyses. The New Hampshire clean updata are also analyzed in briefer fashionrelative to the whole U.S. (Sheavly,1996a) and international (Sheavly,1996b) clean up efforts. The PiscataquaRiver Watershed Council is currentlyconducting a project with the PiscataquaRegion Council on Marine Debris toreduce marine debris, especially bulkdebris, through educational efforts(GOMC, 1997).

A recent review of historical marinedebris distribution, temporal trends andsources of marine debris in the Gulf ofMaine provides further analysis of datafrom New Hampshire, as well as identifi-cation of a range of policy approachesfor addressing the issue (Hoagland andKite-Powell, 1997). In general, it appearsthat New Hampshire, along with north-ern Massachusetts and parts of Nova Sco-tia, have relatively high densities ofnearshore debris compared to Maine andsouthern Massachusetts. Since 1989, both

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Index of Density (items/mile cleaned)

1989 1990 1991 1992 1993 1994 1995

FIGURE 2.44Index of bottles and associated items in marine debris from Maine, New Hampshire and Massa-chusetts, based on CMC data.

Maine and Massachusetts, which havebottle container laws, had slight reduc-tions in beverage container debris whileNew Hampshire showed no reduction(Figure 2.44). Onshore sources of debrisaccounted for 80-85% of all debris, withmuch less coming from offshore sources(including commercial fishing gear).

2.6.5 OTHER CONTAMINANTS

The highest levels of ground-level ozone(O3) in New Hampsire are in the Sea-coast, where transport from largeupwind urban areas is the greatest(NHCRP, 1997). The statewide averagelevel, 0.047 ppm, has not changed muchsince 1990, and the range has been 0.45to 0.5 ppm. The annual frequency ofexceedences at individual locations hasranged from 0 in 1992 to 4 in 1991, with3 in 1995.

Carbon monoxide (CO) is monitoredin Manchester and Nashua. Levelsappeared to improve during the 1990s.Air particulates have been monitored at15 stations. From 1990-1995, none of

them exceeded the standard. Particulatelead was monitored at 5 stations up to1993, when monitoring ceased due todocumented declines in response toremoval of lead from gasoline.

Radon has been tested using hometest kits since 1987. The action guidelineis 4.0 pCi/l. Statewide, the geometricmean level is 2.8 pCi/l, and 36% of sam-ples were > 3.9 pCi/l (NHCRP, 1997). Thegeometric means and percentage of sam-ples > 3.9 pCi/l are 3.0 pCi/l and 38% forRockingham County, and 3.6 pCi/l and44% in Strafford County. Strafford Coun-ty ranks second and Rockingham Coun-ty is fourth amongst other state counties.

Data are kept on accidental chemicalreleases, which includes infectiousagents, chemicals or radiological haz-ards. These usually occur at fixed sites oron roadways. The accidents usuallyinvolve release of petroleum products(77%) and toxic materials (15%). In 1993,Rockingham County had 138 events, themost of any county in the state, and Straf-ford County had 61. The statewide aver-age from 1990 to 1994 was 373 events.

Chlorine is added to municipal drink-ing water (and WWTF effluent) as a nec-essary disinfection agent to kill possiblemicrobial pathogens. However, the chlo-rine is highly reactive and can formpotentially toxic chlorinated organiccompounds, including chloroform, in thepresence of naturally occurring organiccompounds in water. The MaximumContaminant Level (MCL) for chloroformis 5 µg/l. Chloroform was monitored in12 municipal drinking water systems,including six in the coastal region, during1995-1996 (NHCRP, 1997). The averagechloroform concentration and risk (asnumber of excess cancers in one millionpeople) were 44.2 µg/l and 3.17 cancersin Somersworth, 35.8 µg/l and 2.56 can-cers in Exeter, 33 µg/l and 2.36 cancersin Portsmouth, 20.2 µg/l and 1.45 cancersin Rochester, and 17.7 µg/l and 1.28 can-cers in Durham. All of these concentra-tions were greater than the MCL. Thehighest levels statewide were detected atKeene (49.8 µg/l), and Clairmont had thelowest levels (1.1 µg/l) and the only oneunder the MCL.

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The review of technical information onthe status and trends for water quali-

ty in coastal New Hampshire showed agreat deal of existing information for thedifferent issues involved. Despite the

abundance of information, much is stillnot understood and a number of issuesare still significant. This section is a sum-mary of what is known and what infor-mation gaps still exist.

2.7

SUMMARY OF FINDINGS

FINDINGS

� There has been a general improvement in water quality in freshwater rivers andstreams in coastal New Hampshire, in large part due to improvements in sewagetreatment facilities. In 1996, all uses are fully supported in 100% of Coastal Basinand 99% of the Piscataqua River Basin streams and rivers.

� The water quality in the coastal shoreline and open ocean areas of the State’swaters has improved to where they are also fully supporting all uses in 1996.Slower progress in estuarine waters, where uses are limited by numerous contam-inants, has occurred.

� Fecal contamination levels have decreased in all coastal waters during the lastdecade as a result of improvements in wastewater treatment facilities.

� The spatial and temporal distribution of bacterial indicators in estuarine watershas been well documented in most areas. There are clearly sources of fecal con-tamination that persist in all areas of coastal New Hampshire.

� Fecal bacterial contamination is typically present at higher concentrations duringlow tide and after significant rainfall/runoff events.

� The major source of fecal contaminants in runoff is direct sewage contaminationfrom leaky pipes and illicit connections in urban sewage pipe systems. Thesesources are also significant during dry weather.

� Other documented sources of fecal contamination include wastewater treatmentfacilities, septic systems, stormwater control systems and agricultural activities. Sig-nificant non-human sources of contamination other than from agricultural activi-ties have not been documented.

� Recent sanitary surveys have expanded shellfish harvesting in areas with suitablylow levels of fecal contamination.

� Indigenous bacterial pathogens, especially Vibrio spp., are present at relativelyhigh levels in the Great Bay Estuary when water temperatures are warm.

� Tributaries to New Hampshire’s estuaries have storm-related problems with tracemetal contamination. Studies have shown how these contaminants have beentransported, often in association with suspended sediments, throughout the down-stream waters from tributaries.

� An historical database for sediment contaminants provides evidence for wide-spread contamination with trace metals and toxic organic compounds, and local-ized areas of high concentrations of these contaminants.

� Runoff from impervious surfaces is a significant source of both trace metal andtoxic organic contaminants.

� Superfund sites located in close proximity to estuarine waters have had significanthistorical contamination and may continue to be sources affecting water quality.

� The large volume and trafficking of petroleum products through the Port of NewHampshire has resulted in numerous significant oil spills that have had directlyadverse effects on estuarine biota.

� Atmospheric deposition of mercury is a significant concern in New Hampshire,while VOC emissions have been reduced.

� Models for predicting the fate of oil spills, trace metals and fecal contaminationhave been developed for numerous areas.

� Elevated tissue concentrations of toxic contaminants in estuarine biota havecaused several consumption advisories. The relatively elevated levels of a numberof contaminants is a critical concern.

� The highest levels of nitrogen and phosphorus occur in late fall through earlyspring throughout the Great Bay Estuary. The lowest levels occur in late springthrough early fall.

� The highest levels of nutrients occur at the heads of tide in the tributaries, wheresources such as upstream freshwater and WWTFs are most prevalent.

� Phosphate concentrations are usually low in freshwater, highest in upstream tidalrivers and low in Great Bay, Little Bay and Portsmouth Harbor.

� There is an inverse relationship between nitrogen concentration and salinity inGreat Bay Estuary.

� Elevated nutrient levels occur in the tributaries of Hampton Harbor, but the con-centrations in the Harbor itself are low. Conditions are expected to improve withthe recently completed disconnection of septic systems in Seabrook.

� Current nitrogen concentrations, including annual means, seasonal patterns, andminimum and maximum concentrations, are similar to or lower than levels in the1970s in most parts of the Great Bay Estuary and its tributaries. The exceptionsare the freshwater portions of the Cocheco and Salmon Falls rivers, both of whichare significantly impacted by WWTF effluent.

� Significant sources of nutrients include WWTFs, stormwater conduits, septic sys-tems, lawns and golf courses, atmospheric deposition, natural organic debris andsediment recycling.

� Nitrogen loading from riverine sources is highest during late fall and early springduring times where rainfall events are more likely to cause runoff from land sur-faces.

� The total nitrogen loaded to the Great Bay Estuary in 1996, based on some meas-urements and other estimations, was 718 tons. Nonpoint sources accounted for48%, point sources 41% and atmospheric deposition 11% of the total. Similar con-tributions from different sources were determined for the Oyster River watershed.

� The estimated nitrogen loading, 718 tons/y, was slightly higher in 1996 than theNOAA estimate of 640 tons/y, published in 1990.

� Loading estimates for the Great Bay Estuary were below limits established forBuzzards Bay, MA.

� In general, the Great Bay Estuary does not exhibit low dissolved oxygen condi-tions in the tidal waters. D.O. can vary from 5 mg/l in summer during earlymorning low tides to 16 mg/l in winter.

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� Areas in the Salmon Falls River can have exceptionally low D.O. and even anox-ia, especially in the downstream freshwater and the upstream tidal portions dur-ing low flow periods in summer.

� Phytoplankton blooms in Great and Little bays can occur in spring and fall.Rather than experiencing distinct peaks, blooms in tidal rivers typically exhibitgradual increases in chlorophyll a concentrations with peaks in late summer orearly fall.

� Intense bloom events have been observed in the Salmon Falls River coincidingwith low D.O. conditions.

� There is no indication of system-wide eutrophication in the Great Bay and Hamp-ton/Seabrook estuaries. Increased nutrient loading could cause problems in theupper tidal reaches of some of the tributary rivers.

� The major source of suspended sediments in the Great Bay Estuary is probablywind and tidal resuspension of subtidal and intertidal mudflat sediments.

� Paralytic shellfish poisoning levels have occasionally exceeded the closure limit of80 µg PSP/100 g tissue in Hampton Harbor, the only monitoring site in NewHampshire. Little other information is available to document other harmful algalbloom events.

NEEDS

� With increasingly sophisticated monitoring and analytical methods being used,previously unidentified contaminants and sources are being detected. Thus, thereis a continuing need to identify and eliminate sources of fecal and other contami-nants that limit uses if coastal and estuarine waters.

� Establishment of a spatially comprehensive water quality monitoring program isneeded to maintain existing harvestable shellfish areas and expand harvesting tonew areas as management strategies to reduce contaminants are implemented.

� Continuing increases in human population and associated development, impervi-ous surfaces and wastewater treatment demands will modify the capacities forwatersheds to process contaminants. A better understanding of watershed factorsand processes that affect the fate and transport of fecal and other contaminants isneeded to frame effective strategies for managing transport of contaminants tosurface waters.

� Studies on the occurrence of indigenous pathogens like Vibrio spp. and biotoxin-producing organisms would be useful for establishing baseline data and predict-ing potentially harmful conditions.

� A coordinated monitoring program that includes periodic analysis of sediments isneeded to determine temporal trends for sediment contaminants. Monitoring foroil spills and atmospheric contaminants should be continued.

� Studies on the biological effects of single and multiple toxic contaminants areneeded for some ‘hot spot’ areas of New Hampshire’s estuaries.

� With increasing human populations in the Seacoast, it is important to continuemonitoring nutrient levels and dissolved oxygen, especially in the tidal river tribu-taries of the State’s estuaries.

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he Great Bay and Hampton/Seabrook estuaries support agreat diversity of plant and ani-

mal taxa including some rare andendangered species. The estuarine habi-tats that provide important functions tothe seacoast are: shellfish beds, mudand sandflats, salt marshes, eelgrassbeds, algal beds including rocky inter-tidal areas, barrier beach and dune sys-tems, subtidal bottom with substrateranging from mud to cobble and boul-ders, and tidal channels. Inventories ofresident and migratory plant and animalspecies, information on habitats, com-munities biology and ecology can befound in a variety of previously pub-lished documents (Nelson, 1982; Shortet al., 1992; NAI, 1977 and 1996; Spran-kle, 1996; Banner and Hayes, 1996). Thelatter two studies provide excellentcharacterizations of important habitats

for selected species. The selection ofspecies discussed was based on a vari-ety of criteria such as being listed asendangered or threatened, economicimportance, inclusion by other signifi-cant inventories, etc. The approachused as the basis for the Banner andHayes (1996) report was developed bythe US Fish and Wildlife Service withthe Gulf of Maine Council on the MarineEnvironment; a detailed description oftheir approach is provided in the report.The purpose of this chapter is to pro-vide an up to date and comprehenisvedescription of New Hampshire’s estuar-ine biota and to report on the status andtrends of species and communities forwhich there is information. The com-munities and species described herewere selected based on abundance,availability of information and on eco-logical and economic importance.

3 LIVING RESOURCES

T

Flounder

GBN

ERR

Estuarine invertebrates consist of pelag-ic forms (zooplankton) as well as ben-

thic (bottom dwelling) forms. Theoccurrence and distribution of speciesvaries both temporally and spatially andare influenced by several factors includ-ing season, water depth, temperature,salinity, and for benthic forms, substra-tum type (i.e. mud/sand versus rock) isalso a major factor.

3.1.1 ZOOPLANKTON

Zooplankton communities have beenexamined in the Great Bay Estuary bygroups including Normandeau Associ-ates, Inc. as part of the impact assess-ment for the Newington GeneratingStation (NAI, 1976), the University ofNew Hampshire (Turgeon, 1976), and inthe Hampton/Seabrook Estuary (NAI,1996) as part of the Seabrook StationEnvironmental Monitoring Program. Listsof zooplankton species for both estuar-ine areas can be found in Appendix I. Ingeneral, the zooplanktionic communitycan be partitioned into groups thatexhibit three basic life history strategies.The holoplankton (e.g. copepods) areplanktonic throughout their entire lifecycle, while the meroplankton includethe swimming larvae of species that arebenthic as juveniles and adults (eg.,bivalves, gastropods, decapod crus-taceans). The tychoplankton includespecies such as mysids and harpactacoidcopepods that alternate between a ben-thic and pelagic/planktonic existence.

The abundance and species compo-sition of the zooplankton communitiesare temporally and spatially variable.Seasonally, their abundance increasesthroughout the spring, peaking in earlysummer and declining sharply in latersummer. Spatially, the number of speciesdecreases with distance from the openocean. Data gathered by NAI (1976) inGreat Bay indicate that holoplanktonaccounted for 73% of the taxa. The dom-inants holoplankton were copepod nau-plii (29%), Pseudocalanus minutus(14%), Oithona similis (8%), tintinnid

protozoans (7%) and Temora longicornis(2%). Meroplankton forms that onlyenter the zooplankton for reproductioncomprised 22% of the zooplankton,including polychaete (11%), gastropod(5%), bivalve larvae (5%) and cirriped(barnacle) larvae (2%). Tychoplankton,primarily harpacticoid copepods whichare only temporarily suspended in theplankton, represented 5% of zooplank-ton (NAI 1976).

Turgeon (1976) monitored mero-planktonic abundances within the GreatBay Estuary between 1970 and 1973.Bivalve larvae generally decreased fromthe mouth of the Estuary into Great Bay(Turgeon, 1976), and their numbers weregreatest in July and September. Earlystages of bivalve larvae occurred in thenear-surface, while later stages occurredin deeper waters.

Barnacle nauplii (Semibalanus bal-anoides) are one of the first meroplank-ton forms to appear seasonally, duringFebruary, coinciding with the beginningof the spring phytoplankton bloom (Tur-geon, 1976). Trochophores and earlystage spionid polychaete larvae appearfrom April through May, having highestdensities within the inner estuary (Tur-geon, 1976). Mollusc larvae are mostabundant during June through July witha second peak in abundance during Sep-tember. Prosobranch veliger numberswere greatest during June and July beingmost abundant within Great Bay. Up to25 veligers/l may occur within Great Bay,predominantly Ilyanassa obsoleta (Tur-geon, 1976). These patterns were consis-tent during 1970-1973 (Turgeon, 1976),although absolute numbers varied fromyear to year.

Two distinct meroplanktonic com-munities were identified by Turgeon(1976), one predominating in the outerestuary and the second in Great Bay,with the two overlapping in the middleof the estuary. Larval populations weremost dense and species compositionmost varied during February to July andSeptember through November, e.g., the

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3.1

ESTUARINE INVERTEBRATES

123

periods occurring between the winterminimum and summer maximum tem-peratures.

Larval abundances of soft-shell clam,Mya arenaria, are seasonally bimodal(Turgeon, 1976). Oyster larvae, as well asthe larvae of several other bivalves,migrate vertically depending upon thetidal stage. Upward movement in thewater column on flood tides and down-ward movement during ebbing tide pro-moted retention of larvae within GreatBay (Turgeon, 1976).

In the Hampton/Seabrook Estuary,zooplankton communities are similar tothe Great Bay Estuary relative to tempo-ral abundance patterns and dominanceby the holoplanktonic copepods Pseudo-calanus sp. and Oithona sp. (NAI, 1996).The meroplanktonic community is high-ly seasonal, with the greatest abundancesoccurring spring through fall. Dominantmeroplanktonic species include the crus-taceans Balanus sp. and Carcinusmeanas and the bivalves Hiatella sp.,Anomia squamula and Mytilis edulis. Lit-tle change in seasonal patterns and com-munity composition has been observedin the past decade.

3.1.2 BENTHIC INVERTEBRATES

Benthic invertebrates include epibenthossuch as motile bottom dwelling taxa (e.gsnails, crabs and lobsters) and sessiletaxa that attach to hard substrates (e.g.oysters, barnacles) as well as infaunalbenthos that burrow in the sediments.Environmental conditions that are impor-tant in influencing invertebrate occur-rence include water depth, substratum,temperature, salinity, etc. Of these, tidalregulated depth creates a divisionbetween intertidal and subtidal popula-tions. Substratum type is a major deter-minant of species composition. Rock andshingle substrata are populated byepibenthic organisms, while mud andsand have both epibenthic and infaunalcomponents.

Infaunal benthic populations canprovide information that is integral todetermining the ecological condition ofestuaries. They are important regulatorsof the deposition and resuspension of

bottom sediments and the exchange ofconstituents between bottom sedimentsand overlying water. Because of theirburrowing and feeding habits, benthicanimals affect the geochemical profilesof sediments and pore waters, particular-ly in higher salinity habitats with finegrained sediments. Extensive data baseson infaunal macrobenthos for most areasof the Great Bay Estuary have been com-piled over the years. During a 1980-1981monitoring program, 91 intertidal and114 subtidal infaunal species were col-lected from 8 stations throughout theGreat Bay Estuary (Nelson, 1981). Aspecies list of Great Bay benthic infaunaappears in Appendix E. Additionalspecies lists, community analyses, tem-poral and spatial abundances can befound in NAI (1972-1980), Nelson (1982)and Webster (1991). More recent data(Armstrong, 1995; Johnston et al., 1994;Grizzle et al, manuscript in preparation;Langan, 1995, 1996) indicate that speciesrichness and dominant species are essen-tially unchanged over the twenty plusyear period (1972-1995). Grizzle et al.(manuscript in preparation) used threeyears of monthly data from four sites inthe Great Bay Estuary to determine thatthroughout the year, biomass and thenumber of individuals can change dra-matically, with peaks in both numbersand total biomass occurring in springand fall. They attribute the low summerpopulations to predation. They alsofound, as did Nelson (1981), that com-munity composition is determined to agreat extent by sediment grain size.Although species dominance can varyspatially and temporally, generallyspeaking the dominant taxa in the GreatBay Estuary are the polychaetes Streblos-pio benedicti, Heteromastus filiformis,Scolopos sp., Pygospio elegans, Aricideacatherinae, oligochaetes, the amphipodAmpelisca abdita/vadorum, and thebivalves Gemma gemma and Macomabalthica. Abundance, number of taxaand species diversity generally increasewith decreasing distance from the opencoast, indicating that fewer species aretolerant of the seasonal temperatureextremes and daily tidal salinity changes,

which can be as much as 18 ppt, in theupper reaches of Great Bay’s tidal tribu-taries (Langan and Jones, 1996).

The species composition and abun-dance of benthic macrofaunal communi-ties were examined at two sites in theHampton/Seabrook Estuary from 1978-1995 to assess changes in the benthiccommunity that could be attributed to theSeabrook Station’s treatment plant dis-charge to Brown’s River (NAI, 1996). Sam-pling was discontinued in May, 1995 dueto the diversion of the treatment plant out-fall to the offshore cooling water tunnel.Sample sites were located in the Brown’sRiver and in Mill Creek. The dominanttaxa at both sites included the polychaetesStreblospio benedicti, Capitella capitata,and Hediste diversicolor and oligiochaetes.Other common taxa included the poly-chaetes Tharyx acutus and Spio setosa andthe soft shelled clam, Mya arenaria.These species are typical for East Coastestuarine areas with fine grained sedi-ments (Watling, 1975) No significant dif-ferences in density, species compositionor species diversity were found betweensample sites or sample years for the studyperiod. The data also indicated that thetreatment plant outfall had little impact onthe infaunal community in Brown’s River.The clam worm, Neanthes virens, is alsocommon in the intertidal areas of Hamp-ton Harbor and supports a limited com-mercial bait industry.

Hardwick-Witman and Mathieson(1983) compared the epibenthic speciescomposition of the rocky intertidal zoneover a gradient extending from themouth of the Piscataqua River into GreatBay. Within Great Bay, the dominantepibenthic intertidal invertebrates wereIlyanassa obsoleta, Geukensia demissa,Crassostrea virginica, Balanus eberneus,Littorina littorea, L. saxatilis and L.obtusata. Large beds of Eastern oysters,Crassostrea virginica, occur within GreatBay Estuary. This species, along with softshelled clams, blue mussels and sea scal-lops will be discussed in more detail in alater section of this report. Other com-mon epibenthic species in the Great BayEstuary include horseshoe crabs (Limu-lus polyphemus), green crabs (Carcinus

meanas ), mud crabs (family Xanthidae),rock crabs (Cancer irroratus) and Amer-ican lobsters (Homarus americanus).

The warm summer waters withinGreat Bay allow the persistence of sever-al invertebrate species that are morecommon further south along the openAtlantic coast (Bousfield and Thomas,1975). One example of such a disjunctwarm-water taxon is the salt marshamphipod Gammarus palustris; itsnorthern distribution limits on the EastCoast of the US are within Great Bay(Gable and Croker, 1977, 1978). Otherexamples of disjunct invertebrate speciesoccurring within the Great Bay includeBalanus improvisus, Crassostrea virgini-ca, Urosalpinx cinerea, Tellina agilis,Molgula manhattensis, Cliona sp. andPolydora sp. (Turgeon, 1976). Such dis-junct taxa may represent relict popula-tions from a warmer period 10,000 to6,000 yr B.P. (Bousfield and Thomas,1975).

3.1.3 SELECTED INVERTEBRATE SPECIES

3.1.3.1 Molluscan Shellfish

The estuaries of New Hampshire areideal habitat for a number of molluscanshellfish species. The Great Bay Estuary,including Little Harbor and the BackChannel area, supports populations ofthe eastern oyster (Crassostrea virgini-ca), European flat or Belon oysters(Ostrea edulis), softshell clams (Mya are-naria), blue mussels (Mytilus edulis),razor clams (Ensis directus), and sea scal-lops (Placopecten magellanicus). Hamp-ton Harbor supports populations ofsoftshell clams and blue mussels. Mollus-can shellfish are not only of economicimportance for commercial and recre-ational harvesting, they are excellentbioindicators of estuarine conditionbecause they are relatively long livedand integrate their environment overtime. Additionally, because they are filterfeeders, they play an important role innutrient cycling, improving water clarity,and in removing significant quantities ofnitrogen and phosphorus from the watercolumn via phytoplankton and organic

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detritus consumption. Epibenthic shell-fish such as mussels, oysters and scallopsprovide valuable habitat for a richassemblage of invertebrates and fishwhile large infaunal bivalves oxygenatesoft sediments with their burrowingactivities. Oysters are considered bymany estuarine ecologists to be a “key-stone” species, and oyster beds in tem-perate estuaries are considered theequivalent of coral reefs in tropical seas.Many studies have shown that speciesdensity, diversity and biomass are signif-icantly greater in oyster beds than onequivalent bottom without oysters. Mol-luscan shellfish play an important role inthe ecology of estuaries and in the localand regional economies.

Eastern Oyster (Crassostrea virginica)

Eastern oysters range from the Gulf ofMexico to Atlantic Canada, though theiroccurrence is continuous only as farnorth as Cape Cod. North of Cape Cod,disjunct populations can be found inNew Hampshire, Maine, the CanadianMaritimes and the province of Quebec.They are primarily an intertidal and shal-low subtidal species and are most abun-dant in estuarine areas with firmsubstrates. Ice scouring in more northernregions limits their occurrence to shallowsubtidal areas. Eastern oysters can toler-ate salinities ranging from 2-3 ppt to fullseawater salinity (34 ppt) though repro-duction is depressed at low salinities.They can also tolerate temperatures rang-ing from -2°C to >30°C, however, feedingceases and respiration is greatlydepressed below 5°C. Unlike somebivalve species such as bay and sea scal-lops, they thrive in areas of high turbidi-ty. Spawning occurs when watertemperatures reach approximately 20°C,though in the more northern portion oftheir range, annual spawning may notalways occur. The planktonic larvaeremain in the water column for 14-20days and settle on hard substrate, with anoticeable preference for the shells oftheir own species. Accounts of earlyEuropean settlers reported that oysterswere very abundant in the Great BayEstuary, and shell middens indicate that

oysters were consumed by native Amer-icans. Though once harvested commer-cially, they now support a popularrecreational fishery in New Hampshire.

The location and dimension of oys-ter beds in the Great Bay Estuary hasbeen discussed in a number of publica-tions dating back to the late 1940’s. Thepresent beds are shown in Figure 3.1.Maps of oyster bed locations can befound in Ayer et al. (1970), Nelson (1981)and Sale et al. (1992). Oyster habitatbased on occurrence and suitability mod-eling has been recently mapped by theU.S. Fish and Wildlife (Banner andHayes, 1996). A map depicting the loca-tion of these beds in 1980 is shown inFigure 1.5. Jackson (1944) gave a gener-al description of the locations of oysterbeds, and described reduction in oysterpopulations due to siltation and pollu-tion. He recommended rejuvenation ofthe oyster beds through shell plantingand cultivation and suggested that GreatBay oysters could become of consider-able commercial importance. Thoughnumbers for acreage and density fromthat period are not reported, it is obviousfrom Jackson’s description that even inthe 1940’s, much of the oyster habitat inthe Great Bay Estuary had already beenlost. Ayer et al (1970) described the loca-tion, acreage and population structure ofGreat Bay oysters and estimated a stand-ing crop of market sized oysters of38,000 bushels. This estimate was calcu-lated using the areal coverage of the allbeds and density and size frequency ofoysters in the Oyster River only, assum-ing equal density and size structure forall beds. Ayer et al. (1970) also studiedspatfall and growth in various locationsand explored the possibility of a seedoyster industry in New Hampshire. Spat-fall was highly variable both spatially andtemporally. He also found that althoughall bivalve shell caught spat, oyster shellproduced the best results. Additionally,he recommended the use of hatcheryreared larvae for seed production as ameans of producing marketable oystersin a shorter period of time.

Nelson (1982) estimated the densityand standing crop of market-sized oys-

ters, and NH F&G conducted additionalestimates on selected beds in 1991 and1993. These data are presented in Table3.1. It is very difficult to determinechange over time from these data. The1970 estimate only calculated standingcrop/acre for the Oyster River bed andapplied this density to a total of 50 acresin the estuary, though the number ofacres for each bed were not defined. TheAdams Point bed, one of the most popu-lar harvest spots in Great Bay, is notincluded in the 1981 estimate, butappears in 1991 and 1993. The 1981 datareports a great abundance of oysters insouthwest Great Bay, a 90% reductionfrom 1981 to 1991, and no mention of

this bed in 1993. More recent surveywork (1996-1997) has failed to locate alarge concentration of oysters in thesouthwest portion of Great Bay, thougha small concentration can be found inthe vicinity of the railroad bridge thatcrosses the Squamscott River. Reductionin areal coverage of some beds is indi-cated by the data from for the Bellamyand Oyster river beds from 1991 to 1993,with a 67% reduction in the BellamyRiver and a 19% reduction in the OysterRiver. Jackson (1944) also mentions a sig-nificant reduction in the size of OysterRiver bed, though precise changes indimension are not reported. Density datafor all sizes of oysters were obtained for

126

Oyster BedsScattered OystersSoft-shell Clams

Great BayShellfish Beds

FIGURE 3.1

Shellfish resources in Great Bay, Little Bayand tributaries.

127

the years 1991, 1993, 1995 and 1996 fortwo beds near Nannie Island and for1993 and 1996 for Adams Point by per-sonnel from the NH Fish and Game.These data are illustrated in Figure 3.2.According to the data, from 1991 to 1996,there has been a 46% reduction in theNannie Island south bed, a 42% reduc-tion in the Nannie Island/WoodmanPoint bed and a 69% reduction in theAdams Point bed.

These data suggest a decline in oys-ter populations in Great Bay. With the

exception of the 1970 data, however, allthese estimates are based on a relativelysmall number of samples and should beconsidered rough estimates at best. Morerecent studies provide improved infor-mation on oyster resources (Langan,1997) and harvest (NHF&G, 1997c).

It is also useful to examine othersources of information when trying todetermine trends in oyster populations. Asurvey of recreational harvesters conduct-ed by Manalo et al (1991) asked therecreational license holders for an esti-

1970 1981 1991 1993Location acres bushels acres bushels acres bushels acres bushels

Nannie Island ? ? 18.5 18193 ? ? 18.5 20,615Adams Point ? ? ? ? ? ? 5.1 8,358Oyster River 7.4 5594 7.4 12,062 7.4 3,369 6 10,038Southwest Great Bay ? ? 9.8 59,122 9.8 6,389 ? ?Bellamy River ? ? 3.1 3,891 3.1 6,865 1 1,074Piscataqua River ? ? 12.3 23,735 12.3 13,135 12.3 5,412

Total Estimated 50 37,800 51.1 117,003 NA 45,497

Acreage and standing crop of adult oysters in the Great Bay Estuary. TABLE 3.1

0

120

80

60

40

20

100

1992 1993 1995 1996

Nannie IslandNannie/Woodman Point

Adams Point

Number per 0.25m2

Density of oyster beds in Great Bay: 1991-1996. FIGURE 3.2

mate of the amount of time it took to har-vest one bushel of oysters prior to andafter 1989. Seventy four percent of therespondents indicated that it took themlonger to harvest their limit after 1989. Amore recent survey in 1997 by NHF&Gasked recreational harvesters their opin-ion about the general abundance of oys-ters in Great Bay. Fifty five percentexpressed the opinion that the abun-dance was lower than in prior years, sixpercent thought is was higher, eighteenpercent reported no change and seven-teen percent didn’t know. A commercialoyster harvester on the Maine side of thePiscataqua River ceased harvesting oper-ations in 1995 after an epizootic of MSXcaused mass mortalities of oysters in theSalmon Falls and Piscataqua rivers. Spin-ney Creek Shellfish, Inc. estimated 90%mortality in the Salmon Falls River beds,and 50-70% mortality in the PiscataquaRiver beds (T. Howell, personal commu-nication). Data collected in the SalmonFalls and upper Piscataqua rivers in 1997support these mortality estimates (Lan-gan, unpublished data). Though systemicMSX infections in the Oyster River andGreat Bay were lower, there is strong evi-dence, in the form of hinged or “boxed”oysters, to suspect that considerable dis-ease related mortalities occurred in allareas of the Great Bay Estuary. Morerecent studies report the presence of MSXand dermo to be throughout the estuary(NHF&G, 1999).

As stated in another section of thisreport, larval recruitment and juvenilesurvival are important factors in main-taining oyster populations. Ayer et al.(1970) indicated that spat settlement inGreat Bay was highly variable both spa-tially and temporally. They also reportedthat the percent of adult oysters spawn-ing varies from year to year. Data col-lected by the Jackson EstuarineLaboratory from 1991 through 1996 indi-cates that light sets occurred in 1991,1992 and 1996, a heavy set occurred in1993 and virtually no set occurred in1994 and 1995 (Dr. R. Langan, unpub-lished). The reasons for poor sets may berelated to meteorological (temperatureand salinity) and biological (sufficient

food for adults and larvae, disease) con-ditions, but may also be related to theamount of available substrate for larvalattachment. MacKenzie (1989) reportedthat the primary limiting factor in deter-mining oyster recruitment is the amountof clean, hard substrate for larval attach-ment. With this in mind, it is interestingto note that the 1997 oyster harvester sur-vey conducted by the Fish and Gamefound that only 27% of recreational har-vesters return shell to the oyster beds.This would certainly support the conceptthat lack of available substrate for larvalsettlement is contributing to the poorspat settlement and juvenile recruitment.Though the lack of consistency in datacollection makes it very difficult to bescientifically certain, it appears that oys-ter populations in the Great Bay Estuaryhave declined in recent years due to acombination of inconsistent recruitmentand disease.

A long-term trend in oyster popula-tions in the Great Bay Estuary is also dif-ficult to determine since there is a lack ofhistorical data. The report by Jackson(1944) certainly indicates that by the mid-twentieth century, oysters populationshad declined significantly due to overhar-vesting, pollution and siltation. Thoughthese conditions have improved greatlyin recent years, it is unlikely that oysterpopulations have increased much sincethe 1940’s. We may never know the orig-inal baseline of oyster abundance, how-ever, it is probably safe to say that oysterpopulations in the Great Bay Estuary area fraction of what they once were.

Diseases of the Eastern Oyster in New Hampshire

The oyster diseases MSX and Dermo,caused by the protozoan parasites Hap-losporidium nelsoni and Perkinsus mari-nus, respectively, have recently beendetected in oysters from the Great BayEstuary. These diseases were oncethought to be limited in their range bytemperature and salinity to the mid-Atlantic region of the U.S., however theiroccurrence has expanded in recent yearsthrough New England and the diseaseorganisms have been identified as far

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129

north as the Damariscotta River in Maine.These diseases have had a major impacton oyster populations in the Gulf of Mex-ico (Dermo) and have crippled the oys-ter industries in Delaware andChesapeake Bays (MSX and Dermo).Both diseases become more virulent dur-ing dry periods in the summer, whenhigh temperature and salinity conditionspersist. The method of transmission ofMSX is unknown, though it is suspectedthat an intermediate host for the infec-tious life stage may be involved. Dermocan be transmitted directly from one oys-ter to another as well as by a wide vari-ety of organisms included many bivalvespecies, though it appears to be infec-tious only to Eastern oysters

The first recorded MSX epizooticcaused by the oyster parasite Hap-losporidium nelsoni occurred in 1995 inthe Great Bay Estuary (Barber et al.,1997), even though the parasite wasidentified in Piscataqua River oysters in1983 (Sherburne and Bean, 1991) andagain in 1994 (B. Barber, unpublisheddata). Unusual mortalities were observedin the Piscataqua River by Maine har-vesters in August, 1995, and sampleswere examined for the H. nelsoni para-site. Samples of adult oysters (74-102mm) were examined from beds in theSalmon Falls River, three sites in the Pis-cataqua River, the Oyster River, AdamsPoint and Nannie Island. The diseaseprevalence, percent of systemic infec-tions and % dead from the disease areshown in Table 3.2. The disease causedthe greatest mortalities in the SalmonFalls River and farthest upstream beds in

the Piscataqua River, with lower preva-lence and % systemic infections withincreasing distance from the PiscataquaRiver. An examination of the climatolog-ical data, water temperature and salinityindicates that the conditions in 1995were favorable for an MSX epizootic.Both temperature and salinity increasedin all areas of the estuary from 1993 -1995 due to drought conditions. The dis-ease caused mortalities in all oyster bedsand significant mortalities in some, andhas had an impact on oyster populationsthat has not been fully assessed. Oystersamples from Nannie Island and FoxPoint were analyzed in April, 1996. A10% prevalence and no systemic infec-tions were found. Samples of April, 1997,broodstock oysters from Fox Point wereexamined and a 17% prevalence of lightinfections was found. Observations ofgaping and recently dead oysters fromNannie Island and Adams Point in thespring of 1997 (R. Langan, personalobservation) indicates the possibility ofcontinued mortalities from the diseasedespite the lower than average salinitiesin 1996 and the first half of 1997. A reg-ular program of monitoring for H. nel-soni and P. marinus is underway(NHF&G, 1999).

The protozoan oyster parasitePerkinsus marinus, the causative agentof the Dermo disease, was identified inoysters from Spinney Creek, Maine inSeptember, 1996. A large percentage ofthe oysters were infected, and some hadheavy infections. No mortalities wereattributed to the disease at that time.Additional samples were obtained in

Mean SystemicShell Height Prevalence Infections Dead

Location Date (mm) % % %

Salmon Falls 10/27/95 81 81 50 83Piscataqua (Power Lines) 10/27/95 74 70 25 64Piscataqua (Sturgeon Creek) 10/27/95 75 65 40 42Piscataqua (Stacy Creek) 10/27/95 77 45 10 25Oyster River 12/18/95 103 50 30 NAAdams Point 11/06/95 95 40 15 NANannie Island 11/06/95 96 15 5 NA

Prevalence, systemic infection and MSX mortalities of oysters in the Great Bay Estuary, 1995. TABLE 3.2

December, 1997, from two sites in thePiscataqua River and Nannie Island inGreat Bay. A “dermo-like” body wasfound in one of 25 oysters from NannieIsland, and 2 of 25 oysters from at Stur-geon Creek. A heavy infection was foundin one of 25 oysters near the “threerivers” point in the Piscataqua River. Noinfected oysters were found (out of 25) atSeal Rock in the Piscataqua River. Thirtyoysters from Fox Point were examined inMarch, 1997 and no infected oysterswere found. Additional diagnostics havebeen conducted in the summer and fallof 1997. A low prevalence of light Dermoinfections have been found in oystersfrom Adams Point, Nannie Island, andthe Oyster River, while a higher preva-lence and one oyster with advancedinfection was found in the PiscataquaRiver. A neoplasia-like body was seenalso by tissue examinations.

Belon or European Flat Oyster (Ostrea edulis)

The Belon oyster, native to WesternEurope and the British Isles, was intro-duced into the Great Bay Estuary in thelate 1970’s by two commercial compa-nies as an aquaculture species, and wasgrown in suspension culture in Little Bay,the Piscataqua River and Little Harbor,and in bottom culture in Spinney Creek.The Belon oyster prefers lower tempera-tures and higher salinities than theindigenous eastern oyster, and thereforehabitat overlap is unlikely. Though simi-lar in many respects to the Eastern oys-ter, O. edulis broods fertilized eggsinternally, and releases larvae at the tro-chophore stage. Spinney Creek, wherethere is still active aquaculture of thisspecies, has a spawning adult populationcapable of producing large natural sets ofoysters, though few juveniles survive inSpinney Creek due to unfavorable tem-peratures in late summer. “Escapees” ofthis species have established natural,reproductive populations in the Pis-cataqua River, Portsmouth Harbor, LittleHarbor, Rye Harbor, areas of the BackBay in Portsmouth and more recently inGosport Harbor at the Isles of Shoals.Though the actual numbers of this

species is unknown, the fact that condi-tions are favorable for maintaining natu-ral populations is interesting from aperspective of commercial aquaculture,since this species is highly valued and ingreat demand.

Softshell Clams (Mya arenaria)

Softshell clams are an infaunal bivalvethat range from the mid-Atlantic regionof the U.S. through the Canadian Mar-itimes. They can be found in substratesranging from gravel to very soft mud, butappear to be most abundant in muddy orsilty sand. Adults may burrow as deep as20 cm into the substrate. They inhabit theintertidal and shallow subtidal areas ofestuaries and coastal bays, and can toler-ate a wide range of temperature andsalinity. Though usually not a numerical-ly dominant member of the infaunalcommunity, in areas of high abundancethey can represent a very large fractionof the infaunal biomass. Spawningoccurs during two periods, spring andlate summer-fall, though the greatest lar-val densities and greatest spat settlementoccurs during the later spawning period.The larvae are planktonic for approxi-mately 21 days. This species was alsoharvested commercially up to the mid20th century, and is now the most popu-lar recreational shellfish species in NewHampshire.

There is a great deal of uncertaintyregarding abundances of softshell clamsin the Great Bay Estuary. The locationsof clam beds were reported by Nelson(1981) (Figure 3.1) and clam habitat,based primarily on suitability indiceswas recently mapped by the U.S. Fishand Wildlife (Banner and Hayes, 1996).Though clams can be found in mostintertidal flats, densities are generallysparse and are spatially and temporallyvariable. There is some amount of recre-ational clamming in Great Bay, howev-er, if a clammer were asked for his orher preferred location in New Hamp-shire, they would undoubtedly chooseHampton Harbor. Jackson (1944)reported acreage of flats in the GreatBay and the NH Fish and Game report-ed the location and abundance of clams

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Clamflat Location Acres Density Total Area Abundance # BushelsNo. #/m2 m2 1200 clams/bu

1 Odiorne: West 0.4 1.6 1,618 2,589 22 Odiorne: East 8.6 4.4 34,796 153,102 183 Witch Creek: Unsuitable substrate4 Triangle 3.2 12:53 12,950 162,264 1355 Wentworth 12.1 2.02 48,968 98,915 826 Seavey 6.4 5.07 25,900 131,313 1 097 Berrys Brook 4.2 4.65 18,817 87,499 73

Total 34.9 5.0 143,049 635,682 530

Softshell clam flat density and abundance in Little Harbor.

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in Great Bay (Nelson, 1981), Thoughseed clams were abundant at most sites,it appears that few survive since theabundance of larger size classes waslow at all sites. The abundance of seedclams may have also been the result ofa particularly heavy set that year. NHFish and Game (1991) also reportedacreage and standing crop of clams inthe Great Bay Estuary in 1991. Thesedata are presented in Table 3.3. A recentstudy provided more recent data onclam populations in the Great Bay Estu-ary (Langan, 1999). Results show mod-erate to high density of clams on thewestern flats of the Salmon Falls Riverand near Sandy Point in Great Bay, andlow density on the eastern shore oflower Little Bay and along southernshoreline of Dover Point in Little Bay.

Jones and Langan (1996c) estimatedclam abundance and spatfall on severalflats in the Little Harbor area. They

found that densities were generally low,despite the presence of suitable habitat,and that recent spatfall was poor. Thesedata are presented in Table 3.4 and thelocations of shellfish resources areshown in Figure 3.3. NH Fish and Game(1991) reported that there were 400acres of clam flats in Little Harbor, theBack Channel area and in SagamoreCreek and a standing stock of 1,600bushels of adult clams. A more recentreport provides an updated database onclam populations in Back Channel (Lan-gan et al., 1999b).

There is currently insufficient datato establish any trends in clam popula-tions in Great Bay or Little Harbor. Fora historical perspective, the report byJackson (1944) stated that clamsdeclined steadily in number between1900 and 1944, and at that time therewas “only a vestige of their formerabundance,” though no quantitative

Jackson (1944) NH F&G (1991) NH F&G (1991)Location Acreage Acreage Total Bushels

Salmon Falls River 125 125 500Cocheco River 140 140 560Piscataqua River 265 265 1060Bellamy River 300 300 1200Oyster River 225 225 900Lamprey River 60 60 240Squamscott River 180 180 720Little Bay 430 380 1520Great Bay 1000 500 2000Total 2725 2175 8700

Softshell clam flat acreage and abundance in Great Bay Estuary. TABLE 3.3

TABLE 3.4

data are available for that period. The locations of clam resources in

Hampton Harbor are illustrated in Figure3.4. Abundance and age composition ofclams from the Hampton River Conflu-ence, Common Island and Seabrook(middle ground) clam flats in HamptonHarbor have been monitored since 1974by Normandeau Associates for the PublicService Company of New Hampshire asa requirement of their license to operatethe Seabrook nuclear power plant. Larvalabundance has been monitored for thesame time period at a nearfield stationoutside the Harbor. This is without adoubt the most complete dataset for

shellfish in New Hampshire and the longterm data are presented in detail in theutilities’ 1996 environmental report (NAI,1996). Since only a summary of the infor-mation is presented here, the reader isreferred to the referenced document formore detail.

Larval Abundance

Mya larvae are present in the water col-umn from May through October andmaximum densities are typically record-ed in late summer or early fall with a sec-ondary peak in early summer. Thistiming of the peak density can vary intiming and magnitude. Larval density has

132

Rye Harbor

LittleHarbor

PortsmouthHarbor

Soft-shelled Clams

FIGURE 3.3

Shellfish resources inPortsmouth, Rye, and Little Harbors.

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been generally lower in the years 1991-1995 than in the period from 1978-1981.Gonadal studies indicate that spawningin Hampton Harbor usually follows theappearance of larvae at offshore stations,indicating that the early larvae are notproduced by local broodstock. Based onthe current patterns in the area, it is like-ly that recruitment of larvae of non-localorigin occurs.

Young of the Year

Young of the year (YOY) clams arenewly settled spat ranging from 1-5 mm.Historically YOY clam density has beenhighly variable both spatially and tempo-

rally in Hampton Harbor. In 1995, YOYdensity on the Seabrook Flat was lowerthan all years since 1974, while on theHampton River confluence flat, densitywas higher than 1991-1994, but lowerthan the 1974-1989 average. Density wasthe second lowest since 1974 on theCommon Island flat. Long term densityappears to have declined slightly since1974, and good sets appear to occurapproximately every three to four years(Figure 3.5).

Spat

Density of spat (6-25 mm), or year oneclams that have successfully overwin-

1

4

3

2

5

1 Angels Creek2 Coles Creek3 Shipyard4 Tide Mill Creek5 The Slough6 Eagle Creek7 Ell Creeks8 Fire Man Creek9 Mussel Bed10 Hampton Falls Depot11 Swins Creek12 Hampton Flats13 Eastmans Slough14 Swains Creek15 Peanut Stand16 Johnny Bragg's Birth17 Nates Stake18 Half Tide Rock19 Common Island20 Sinnies Creek21 Knowles Island22 Middle Ground23 Race Rock24 Gills Rock25 Merrills Point26 Upper Gills Rock27 Great Slough Creek28 Morrill Creek29 Doles Island30 Cross Beach31 Simes Flats32 Crotch Creek33 Dock Creek

1 Common Island2 Hampton/Browns

River Confluence3 Browns River Area4 Middle Ground5 The Willows

Clam Beds

3132

3029

28

26

24 25

27

23

21

20

22

19

16

1518

17

14

13

129

8

6

57

11

4

310

2

1

FIGURE 3.4

Shellfish resources in theHampton Harbor Estuary.

tered, has been variable for the studyperiod, however, it can be stated thatdensity on all flats was highest from 1977through 1981, lowest from 1981 through1989, and although much lower than the1977-81 abundances, peaks in densityoccurred in 1990 and 1994. These peaksin density correspond well to the YOYdensities except for the years from 1983through 1987 where it appears that rea-sonably good sets did not survive thewinter (Figure 3.6).

Juveniles

Juvenile clams (26-50 mm), are morethan likely two year old clams. Theannual density of juveniles correspondswell with spat density with a one yearlag time. Clams of this size were mostabundant from 1979-1981, and havedeclined steadily since, though smallerpeak densities were recorded in 1990and 1995 (Figure 3.7).

Adults

Adult clams (>50 mm) were abundant in1971 through 1975 (Savage and Dunlop1983), declined from 1976-1979, and

reached peak abundances from 1980-1984. The steady sharp decline in abun-dance beginning in 1984 was very likelydue to heavy harvest pressure. A classicpredator prey relationship, where thechange in density of prey is tracked by achange in predator density (with somelag period), exists between the clampopulation and the number of adult clamlicenses sold (Figure 3.8). Closure of theflats in 1989 resulted in minor recoveryof adult clam density on the CommonIsland flat from 1989 to 1995, a muchgreater increase in density in clams onthe Seabrook flat, and little change onthe Hampton River confluence flat,though an increase was recorded from1994-1995. The Common Island flat wasreopened in 1994, however the effects ofrecreational clamming in 1994 and 1995appeared to have little effect on clamdensity (Figure 3.9). A recent studyfocused on removing blue mussels fromflats to improve clam habitats (Langanand Barnaby, 1998).

Predation, particularly of smallclams, can greatly affect the survival ofclams to harvestable size. The green

134

Seabrook Stationin Operation

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 1-5mm

Flat 1

Flat 2

Flat 4

FIGURE 3.5 Annual mean log10(x+1) density (number per ft2) of clams 1-5 mm length: 1974-1995. Data from NAI (1995)

135

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 6-25mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

Annual mean log10(x+1) density (number per ft2) of clams 6-25 mm length: 1974-1995. FIGURE 3.6Data from NAI (1995).

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 26-50mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

Annual mean log10(x+1) density (number per ft2) of clams 26-50 mm length: 1974-1995. FIGURE 3.7Data from NAI (1995).

136

0

5000

10000

15000

Bushels

Licenses

1971 1973 1975 1977 1979 1981 1983 1985 1987

FIGURE 3.8 Number of clam licenses and the adult clam standing crop (bushels) in Hampton-Seabrook Harbor: 1971-1987. Data from NAI (1995).

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams >50mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

FIGURE 3.9 Annual mean log10(x+1) density (number per ft2) of clams >50 mm length: 1974-1995. Data from NAI (1995).

137

crab, a major predator of Mya, has beenhighly variable over time in HamptonHarbor, but unlike human predators,their numbers are influenced by mini-mum winter water temperatures ratherthan prey (clam) abundance. Even inyears of low crab abundance, thereappears to be sufficient numbers of crabsin the Harbor to impact juvenile clamabundance. Other predators includenematodes, horseshoe crabs and birds.Though massive sets of clams could“breakthrough” and overwhelm preda-tion pressure, it is unlikely that this willhappen without substantial natural orartificial reseeding and predator protec-tion (Savage and Dunlop, 1983).

Ultimately, it appears that the con-trolling factors determining clam popula-tions in Hampton Harbor are larvalsettlement, predation, prevalence of sar-comatous neoplasia (Hampton River flat)and harvest pressure. Savage and Dun-lop (1983) stated that unless and seedclams are protected from predators andharvest pressure on adult clams is con-trolled, it would be very difficult for evenlarge sets of clams to overcome the rateof predation and produce increasedquantities of adult clams.

Softshell Clam Diseases: Sarcomatous neoplasia

Sarcomatous neoplasia, a lethal form ofleukemia in clams, has the potential tocause serious mortalities in the softshellclams. The infection has been observedin relatively pristine waters, however it issuspected that the rate of infection isenhanced by pollution.

Sarcomatous neoplasia was observedin Hampton Harbor clam populations inOctober, 1986 and February, 1987 fromthe Common Island (6%) and HamptonRiver confluence (27%) flats (NAI, 1996).No infections were found on theSeabrook flat (middle ground). Clam sur-veys in 1987 indicated that juvenile andadult densities were reduced by 50% inthe two flats where disease was identi-fied, while the population wasunchanged on the middle ground. It issuspected that the reduced densities

resulted from disease related mortalities.In November, 1989, twelve of fifteenclams (80%) from the Hampton Riverwere infected. From 1990-1995, adultclam densities quadrupled in the middleground, while Common Island densitiesdid not change, and Hampton River den-sity decreased by 50%. It is suspectedthat disease may have contributed to theobserved reductions. Clams in the GreatBay Estuary have not been examined forneoplasia.

Blue Mussels (Mytilis edulis)

The blue mussel is widely distributed inthe North Atlantic and occurs in Europeas well as North America. On the EastCoast of the U.S., it ranges from CapeHatteras to the Arctic Circle. Musselsinhabit the intertidal and subtidal zonesof estuaries and the open coast. Thoughprimarily a shallow water species, theyare sometimes found at considerabledepths. They can tolerate temperaturesranging from -2°C to 25°C and salinitiesranging from 5 ppt to 35 ppt, thoughprolonged expose to salinities below 15ppt are lethal. Spawning can occur yearround, though the peak spawning peri-od is June through August. Like otherbivalves, the larvae are planktonic andremain in the water column for three tofive weeks. Initial settlement occurs inshallow water on any firm substrate,however, newly attached juvenile mus-sels can detach their byssal threads anddrift with the currents in search of othersuitable attachment surfaces. Thoughmussels are harvested in large quantitiesand are an important aquaculturespecies in Europe, Canada and otherparts of the world, they are largelyignored as a food species in New Eng-land. They are considered by many tobe a nuisance species since colonizationleads to fouling of industrial and coastalstructures, as well as the hulls of ships.

Blue mussels can be found in theGreat Bay Estuary attached to any hardsubstrate in the intertidal and subtidalzones, and also colonize intertidal flats inscattered clumps and contiguous mats.Though during high salinity periods

mussels may be found in most areas ofthe estuary, their limited tolerance forlow salinity limits their permanentupstream distribution to the area aroundDover Point. Mussels are most abundantin the lower Piscataqua River, Ports-mouth Harbor and Little Harbor. Thelocation of some mussel beds in thelower estuary was identified as part ofthe Ecological Risk Assessment study forthe Portsmouth Naval Shipyard. Density,size and condition index of mussels froma number of sites was measured for thisstudy (Johnston et al., 1994). Banner andHayes (1996) mapped blue mussel habi-tat using a suitability index model, how-ever, the lower estuary where musselsare most abundant was not included intheir study.

Long term records of larval abun-dance and juvenile settlement of bluemussels have been maintained as part ofthe PSNH environmental studies pro-gram by Normandeau Associates (NAI,1996). Mussel larvae are a dominanttaxon in the nearshore plankton commu-nity and are the dominant noncolonialtaxon on shallow depth fouling panels.Density of larvae has increased in recentyears, and though settlement variesannually, in general it has increased inrecent years as well. Mussels can befound in the estuary attached to hardsubstrate in both the intertidal and subti-dal zones, and can form extensive bedson tidal flats. Banner and Hayes (1996)have mapped mussel habitat usingoccurrence and suitability indices. Themost prominent beds are located in theHampton River, Blackwater River, and onthe Seabrook middle ground clam flat.There is no scientifically documentedchange in abundance, though there isinformation (P. Tilton, personal commu-nication) that the coverage of mussels onthe Seabrook flat has increased in recentyears. Mussel density on the flats inSeabrook can be as high as 3500/m2

(Langan and Barnaby, 1998). Recentdevelopments in new culture techniques,combined with increased market valueand an abundant natural seed supplymakes this species an ideal candidate foraquaculture development.

Sea Scallops (Placopecten magellanicus)

Though primarily an oceanic species, seascallops can be found in the higher salin-ity areas of bays and estuaries in NewEngland below a depth of 5 meters. Sev-eral scallop beds are located in the lowerPiscataqua River and Portsmouth Harborand include the area between Salaman-der Point and Fort Point, in Spruce Creekand off Fort McClarey in Kittery, Maine.Langan (1994) examined the density, sizestructure and movements of scallops inthe Fort Point area using SCUBA surveysand mark and recapture studies. Meandensity was 1.3 scallops/m2 and with theexception of few small (10-20 mm) indi-viduals, the population had a normal dis-tribution. Small scallops are difficult tosee and may have been overlooked bydivers. Scallop movement is greater forthe 40-60 mm sized animals than smalleror larger individuals. Some large scallopswere found within 100 meters of therelease site a year after tagging. A projectwhich began in 1996 (Langan 1997) isinvestigating the spawning time, spatfalland growth and mortality of scallops insuspension and bottom culture. Thespawning period in 1996, based ongonadal/ somatic index (GSI), com-menced in late July and spat settlementbegan in October. Onion bag/monofila-ment type spat collectors were used tocapture larvae. Some collectors wereretrieved in March and scallops from 4-10 mm were retrieved. These scallopsand approximately one thousand 25 mmindividuals were placed in suspensionculture to measure growth and mortality.Natural enhancement of the bottomunder the collectors was assessed in thesummer of 1997.

Scallops are fished commercially withtowed dredges from November 1 to April14, and are harvested commercially andrecreationally using SCUBA. Other thanthe 1994 survey at Fort Point, there is lit-tle information on scallop density or pop-ulation change over time. Commercialfishermen indicate, however, that there isa great deal of variation in scallop abun-dance both temporally and spatially (P.Flanigan, personal communication).

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139

Other Bivalve Species

Though there is no documented infor-mation on population densities andtrends, several other bivalve speciescommon to New Hampshire estuariesshould be mentioned. The deposit feed-ing clam Macoma balthica is common inall areas of Great Bay and Hampton Har-bor and the siphon of this clam is afavored prey item of juvenile winterflounder (Armstrong, 1996). Razor clams(Ensis directus) can be locally abundantin subtidal areas of Great Bay (Nelson,1981), and the ribbed mussel (Geukensiademissus) is also common in lower salin-ity and marsh areas of the Great Bay(Nelson, 1981) and Hampton/Seabrookestuaries. The gem clam, Gemmagemma, a very small bivalve, can be thedominant infaunal taxon in the sandierareas of Great Bay.

3.1.3.2 Crustaceans

American Lobsters

The American lobster is the largest crus-tacean inhabiting New Hampshire’s estu-aries and coastal zone. They are thetarget of a large and valuable commercialfishery which will be discussed in a latersection of this report. Though primarily acoastal and oceanic species, lobstersinhabit many coastal bays and estuaries.They range from the mid-Atlantic statesthrough Newfoundland, though in theirsouthern range, they are found in great-est abundance in deeper offshore waters.Though most often fished in shallowwaters (<100 ft), lobsters inhabit watersas deep as 1,500 ft. Lobsters are omnivo-rous, feeding on molluscs, urchins,starfish, crabs and even other lobsters.They in turn are preyed upon by seals,groundfish (cod) and other large preda-tory fish such as striped bass. The adultsundergo a seasonal migration, movinginshore in spring and offshore in the fall,though within that time period, they maymove about a great deal within estuaries(Dr. S. Jury, personal communication).Spawning occurs by means of internalfertilization when the female has recent-ly molted, and the fertilized eggs are

extruded one year after molting. Thefemales carry the fertilized eggs undertheir abdomen for up to one year. Theeggs hatch and are released into thewater column in late spring/early sum-mer in near shore areas, and the plank-tonic larvae go through several moltstages before settling to the bottom. Thepreferred juvenile settlement substrate isrock-cobble, (Wahle and Steneck 1991,1992) though older juveniles can befound inhabiting any type of substratewhere shelter (boulders, rocks, cobble,mud burrows) can be found. Lobstersreach commercial size after 15-20 moltsor in 6-9 years. Despite increased fishingpressure in recent years, lobster popula-tions are relatively stable. More informa-tion on lobster abundance is presentedin Chapter 4.

Crabs

Several species of crabs can be found inabundance in New Hampshire’s estuariesand coastal areas. Most prominent arethe rock crab (Cancer irroratus ) and thegreen crab (Carcinus maenas) thoughthe small mud crabs of the generaPanopeus and Rhythropanopeus are alsovery abundant. There is some commer-cial harvesting of rock crabs for humanconsumption and green crabs for bait,however, their economic importance isnegligible.

3.1.3.3 Horseshoe Crabs (Limulus polyphemus)

The horseshoe crab (Limulus polyphe-mus) is not a true crab, and among thearthropods is more closely related to thearachnids (spiders, scorpions) than crus-taceans. Horseshoe crabs are abundantin Great Bay and occur in lower numbersin Hampton Harbor. They are most con-spicuous in the month of June, whenthey mate in large numbers during thespring flood tides and deposit their eggson the beach. The eggs are preyed uponby several species of shore birds andrepresent a major food source for somespecies. Horseshoe crabs excavate largefeeding pits in soft substrates, consumingthe worms, molluscs and crustaceans.

mate of the amount of time it took to har-vest one bushel of oysters prior to andafter 1989. Seventy four percent of therespondents indicated that it took themlonger to harvest their limit after 1989. Amore recent survey in 1997 by NHF&Gasked recreational harvesters their opin-ion about the general abundance of oys-ters in Great Bay. Fifty five percentexpressed the opinion that the abun-dance was lower than in prior years, sixpercent thought is was higher, eighteenpercent reported no change and seven-teen percent didn’t know. A commercialoyster harvester on the Maine side of thePiscataqua River ceased harvesting oper-ations in 1995 after an epizootic of MSXcaused mass mortalities of oysters in theSalmon Falls and Piscataqua rivers. Spin-ney Creek Shellfish, Inc. estimated 90%mortality in the Salmon Falls River beds,and 50-70% mortality in the PiscataquaRiver beds (T. Howell, personal commu-nication). Data collected in the SalmonFalls and upper Piscataqua rivers in 1997support these mortality estimates (Lan-gan, unpublished data). Though systemicMSX infections in the Oyster River andGreat Bay were lower, there is strong evi-dence, in the form of hinged or “boxed”oysters, to suspect that considerable dis-ease related mortalities occurred in allareas of the Great Bay Estuary. Morerecent studies report the presence of MSXand dermo to be throughout the estuary(NHF&G, 1999).

As stated in another section of thisreport, larval recruitment and juvenilesurvival are important factors in main-taining oyster populations. Ayer et al.(1970) indicated that spat settlement inGreat Bay was highly variable both spa-tially and temporally. They also reportedthat the percent of adult oysters spawn-ing varies from year to year. Data col-lected by the Jackson EstuarineLaboratory from 1991 through 1996 indi-cates that light sets occurred in 1991,1992 and 1996, a heavy set occurred in1993 and virtually no set occurred in1994 and 1995 (Dr. R. Langan, unpub-lished). The reasons for poor sets may berelated to meteorological (temperatureand salinity) and biological (sufficient

food for adults and larvae, disease) con-ditions, but may also be related to theamount of available substrate for larvalattachment. MacKenzie (1989) reportedthat the primary limiting factor in deter-mining oyster recruitment is the amountof clean, hard substrate for larval attach-ment. With this in mind, it is interestingto note that the 1997 oyster harvester sur-vey conducted by the Fish and Gamefound that only 27% of recreational har-vesters return shell to the oyster beds.This would certainly support the conceptthat lack of available substrate for larvalsettlement is contributing to the poorspat settlement and juvenile recruitment.Though the lack of consistency in datacollection makes it very difficult to bescientifically certain, it appears that oys-ter populations in the Great Bay Estuaryhave declined in recent years due to acombination of inconsistent recruitmentand disease.

A long-term trend in oyster popula-tions in the Great Bay Estuary is also dif-ficult to determine since there is a lack ofhistorical data. The report by Jackson(1944) certainly indicates that by the mid-twentieth century, oysters populationshad declined significantly due to overhar-vesting, pollution and siltation. Thoughthese conditions have improved greatlyin recent years, it is unlikely that oysterpopulations have increased much sincethe 1940’s. We may never know the orig-inal baseline of oyster abundance, how-ever, it is probably safe to say that oysterpopulations in the Great Bay Estuary area fraction of what they once were.

Diseases of the Eastern Oyster in New Hampshire

The oyster diseases MSX and Dermo,caused by the protozoan parasites Hap-losporidium nelsoni and Perkinsus mari-nus, respectively, have recently beendetected in oysters from the Great BayEstuary. These diseases were oncethought to be limited in their range bytemperature and salinity to the mid-Atlantic region of the U.S., however theiroccurrence has expanded in recent yearsthrough New England and the diseaseorganisms have been identified as far

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129

north as the Damariscotta River in Maine.These diseases have had a major impacton oyster populations in the Gulf of Mex-ico (Dermo) and have crippled the oys-ter industries in Delaware andChesapeake Bays (MSX and Dermo).Both diseases become more virulent dur-ing dry periods in the summer, whenhigh temperature and salinity conditionspersist. The method of transmission ofMSX is unknown, though it is suspectedthat an intermediate host for the infec-tious life stage may be involved. Dermocan be transmitted directly from one oys-ter to another as well as by a wide vari-ety of organisms included many bivalvespecies, though it appears to be infec-tious only to Eastern oysters

The first recorded MSX epizooticcaused by the oyster parasite Hap-losporidium nelsoni occurred in 1995 inthe Great Bay Estuary (Barber et al.,1997), even though the parasite wasidentified in Piscataqua River oysters in1983 (Sherburne and Bean, 1991) andagain in 1994 (B. Barber, unpublisheddata). Unusual mortalities were observedin the Piscataqua River by Maine har-vesters in August, 1995, and sampleswere examined for the H. nelsoni para-site. Samples of adult oysters (74-102mm) were examined from beds in theSalmon Falls River, three sites in the Pis-cataqua River, the Oyster River, AdamsPoint and Nannie Island. The diseaseprevalence, percent of systemic infec-tions and % dead from the disease areshown in Table 3.2. The disease causedthe greatest mortalities in the SalmonFalls River and farthest upstream beds in

the Piscataqua River, with lower preva-lence and % systemic infections withincreasing distance from the PiscataquaRiver. An examination of the climatolog-ical data, water temperature and salinityindicates that the conditions in 1995were favorable for an MSX epizootic.Both temperature and salinity increasedin all areas of the estuary from 1993 -1995 due to drought conditions. The dis-ease caused mortalities in all oyster bedsand significant mortalities in some, andhas had an impact on oyster populationsthat has not been fully assessed. Oystersamples from Nannie Island and FoxPoint were analyzed in April, 1996. A10% prevalence and no systemic infec-tions were found. Samples of April, 1997,broodstock oysters from Fox Point wereexamined and a 17% prevalence of lightinfections was found. Observations ofgaping and recently dead oysters fromNannie Island and Adams Point in thespring of 1997 (R. Langan, personalobservation) indicates the possibility ofcontinued mortalities from the diseasedespite the lower than average salinitiesin 1996 and the first half of 1997. A reg-ular program of monitoring for H. nel-soni and P. marinus is underway(NHF&G, 1999).

The protozoan oyster parasitePerkinsus marinus, the causative agentof the Dermo disease, was identified inoysters from Spinney Creek, Maine inSeptember, 1996. A large percentage ofthe oysters were infected, and some hadheavy infections. No mortalities wereattributed to the disease at that time.Additional samples were obtained in

Mean SystemicShell Height Prevalence Infections Dead

Location Date (mm) % % %

Salmon Falls 10/27/95 81 81 50 83Piscataqua (Power Lines) 10/27/95 74 70 25 64Piscataqua (Sturgeon Creek) 10/27/95 75 65 40 42Piscataqua (Stacy Creek) 10/27/95 77 45 10 25Oyster River 12/18/95 103 50 30 NAAdams Point 11/06/95 95 40 15 NANannie Island 11/06/95 96 15 5 NA

Prevalence, systemic infection and MSX mortalities of oysters in the Great Bay Estuary, 1995. TABLE 3.2

December, 1997, from two sites in thePiscataqua River and Nannie Island inGreat Bay. A “dermo-like” body wasfound in one of 25 oysters from NannieIsland, and 2 of 25 oysters from at Stur-geon Creek. A heavy infection was foundin one of 25 oysters near the “threerivers” point in the Piscataqua River. Noinfected oysters were found (out of 25) atSeal Rock in the Piscataqua River. Thirtyoysters from Fox Point were examined inMarch, 1997 and no infected oysterswere found. Additional diagnostics havebeen conducted in the summer and fallof 1997. A low prevalence of light Dermoinfections have been found in oystersfrom Adams Point, Nannie Island, andthe Oyster River, while a higher preva-lence and one oyster with advancedinfection was found in the PiscataquaRiver. A neoplasia-like body was seenalso by tissue examinations.

Belon or European Flat Oyster (Ostrea edulis)

The Belon oyster, native to WesternEurope and the British Isles, was intro-duced into the Great Bay Estuary in thelate 1970’s by two commercial compa-nies as an aquaculture species, and wasgrown in suspension culture in Little Bay,the Piscataqua River and Little Harbor,and in bottom culture in Spinney Creek.The Belon oyster prefers lower tempera-tures and higher salinities than theindigenous eastern oyster, and thereforehabitat overlap is unlikely. Though simi-lar in many respects to the Eastern oys-ter, O. edulis broods fertilized eggsinternally, and releases larvae at the tro-chophore stage. Spinney Creek, wherethere is still active aquaculture of thisspecies, has a spawning adult populationcapable of producing large natural sets ofoysters, though few juveniles survive inSpinney Creek due to unfavorable tem-peratures in late summer. “Escapees” ofthis species have established natural,reproductive populations in the Pis-cataqua River, Portsmouth Harbor, LittleHarbor, Rye Harbor, areas of the BackBay in Portsmouth and more recently inGosport Harbor at the Isles of Shoals.Though the actual numbers of this

species is unknown, the fact that condi-tions are favorable for maintaining natu-ral populations is interesting from aperspective of commercial aquaculture,since this species is highly valued and ingreat demand.

Softshell Clams (Mya arenaria)

Softshell clams are an infaunal bivalvethat range from the mid-Atlantic regionof the U.S. through the Canadian Mar-itimes. They can be found in substratesranging from gravel to very soft mud, butappear to be most abundant in muddy orsilty sand. Adults may burrow as deep as20 cm into the substrate. They inhabit theintertidal and shallow subtidal areas ofestuaries and coastal bays, and can toler-ate a wide range of temperature andsalinity. Though usually not a numerical-ly dominant member of the infaunalcommunity, in areas of high abundancethey can represent a very large fractionof the infaunal biomass. Spawningoccurs during two periods, spring andlate summer-fall, though the greatest lar-val densities and greatest spat settlementoccurs during the later spawning period.The larvae are planktonic for approxi-mately 21 days. This species was alsoharvested commercially up to the mid20th century, and is now the most popu-lar recreational shellfish species in NewHampshire.

There is a great deal of uncertaintyregarding abundances of softshell clamsin the Great Bay Estuary. The locationsof clam beds were reported by Nelson(1981) (Figure 3.1) and clam habitat,based primarily on suitability indiceswas recently mapped by the U.S. Fishand Wildlife (Banner and Hayes, 1996).Though clams can be found in mostintertidal flats, densities are generallysparse and are spatially and temporallyvariable. There is some amount of recre-ational clamming in Great Bay, howev-er, if a clammer were asked for his orher preferred location in New Hamp-shire, they would undoubtedly chooseHampton Harbor. Jackson (1944)reported acreage of flats in the GreatBay and the NH Fish and Game report-ed the location and abundance of clams

130

Clamflat Location Acres Density Total Area Abundance # BushelsNo. #/m2 m2 1200 clams/bu

1 Odiorne: West 0.4 1.6 1,618 2,589 22 Odiorne: East 8.6 4.4 34,796 153,102 183 Witch Creek: Unsuitable substrate4 Triangle 3.2 12:53 12,950 162,264 1355 Wentworth 12.1 2.02 48,968 98,915 826 Seavey 6.4 5.07 25,900 131,313 1 097 Berrys Brook 4.2 4.65 18,817 87,499 73

Total 34.9 5.0 143,049 635,682 530

Softshell clam flat density and abundance in Little Harbor.

131

in Great Bay (Nelson, 1981), Thoughseed clams were abundant at most sites,it appears that few survive since theabundance of larger size classes waslow at all sites. The abundance of seedclams may have also been the result ofa particularly heavy set that year. NHFish and Game (1991) also reportedacreage and standing crop of clams inthe Great Bay Estuary in 1991. Thesedata are presented in Table 3.3. A recentstudy provided more recent data onclam populations in the Great Bay Estu-ary (Langan, 1999). Results show mod-erate to high density of clams on thewestern flats of the Salmon Falls Riverand near Sandy Point in Great Bay, andlow density on the eastern shore oflower Little Bay and along southernshoreline of Dover Point in Little Bay.

Jones and Langan (1996c) estimatedclam abundance and spatfall on severalflats in the Little Harbor area. They

found that densities were generally low,despite the presence of suitable habitat,and that recent spatfall was poor. Thesedata are presented in Table 3.4 and thelocations of shellfish resources areshown in Figure 3.3. NH Fish and Game(1991) reported that there were 400acres of clam flats in Little Harbor, theBack Channel area and in SagamoreCreek and a standing stock of 1,600bushels of adult clams. A more recentreport provides an updated database onclam populations in Back Channel (Lan-gan et al., 1999b).

There is currently insufficient datato establish any trends in clam popula-tions in Great Bay or Little Harbor. Fora historical perspective, the report byJackson (1944) stated that clamsdeclined steadily in number between1900 and 1944, and at that time therewas “only a vestige of their formerabundance,” though no quantitative

Jackson (1944) NH F&G (1991) NH F&G (1991)Location Acreage Acreage Total Bushels

Salmon Falls River 125 125 500Cocheco River 140 140 560Piscataqua River 265 265 1060Bellamy River 300 300 1200Oyster River 225 225 900Lamprey River 60 60 240Squamscott River 180 180 720Little Bay 430 380 1520Great Bay 1000 500 2000Total 2725 2175 8700

Softshell clam flat acreage and abundance in Great Bay Estuary. TABLE 3.3

TABLE 3.4

data are available for that period. The locations of clam resources in

Hampton Harbor are illustrated in Figure3.4. Abundance and age composition ofclams from the Hampton River Conflu-ence, Common Island and Seabrook(middle ground) clam flats in HamptonHarbor have been monitored since 1974by Normandeau Associates for the PublicService Company of New Hampshire asa requirement of their license to operatethe Seabrook nuclear power plant. Larvalabundance has been monitored for thesame time period at a nearfield stationoutside the Harbor. This is without adoubt the most complete dataset for

shellfish in New Hampshire and the longterm data are presented in detail in theutilities’ 1996 environmental report (NAI,1996). Since only a summary of the infor-mation is presented here, the reader isreferred to the referenced document formore detail.

Larval Abundance

Mya larvae are present in the water col-umn from May through October andmaximum densities are typically record-ed in late summer or early fall with a sec-ondary peak in early summer. Thistiming of the peak density can vary intiming and magnitude. Larval density has

132

Rye Harbor

LittleHarbor

PortsmouthHarbor

Soft-shelled Clams

FIGURE 3.3

Shellfish resources inPortsmouth, Rye, and Little Harbors.

133

been generally lower in the years 1991-1995 than in the period from 1978-1981.Gonadal studies indicate that spawningin Hampton Harbor usually follows theappearance of larvae at offshore stations,indicating that the early larvae are notproduced by local broodstock. Based onthe current patterns in the area, it is like-ly that recruitment of larvae of non-localorigin occurs.

Young of the Year

Young of the year (YOY) clams arenewly settled spat ranging from 1-5 mm.Historically YOY clam density has beenhighly variable both spatially and tempo-

rally in Hampton Harbor. In 1995, YOYdensity on the Seabrook Flat was lowerthan all years since 1974, while on theHampton River confluence flat, densitywas higher than 1991-1994, but lowerthan the 1974-1989 average. Density wasthe second lowest since 1974 on theCommon Island flat. Long term densityappears to have declined slightly since1974, and good sets appear to occurapproximately every three to four years(Figure 3.5).

Spat

Density of spat (6-25 mm), or year oneclams that have successfully overwin-

1

4

3

2

5

1 Angels Creek2 Coles Creek3 Shipyard4 Tide Mill Creek5 The Slough6 Eagle Creek7 Ell Creeks8 Fire Man Creek9 Mussel Bed10 Hampton Falls Depot11 Swins Creek12 Hampton Flats13 Eastmans Slough14 Swains Creek15 Peanut Stand16 Johnny Bragg's Birth17 Nates Stake18 Half Tide Rock19 Common Island20 Sinnies Creek21 Knowles Island22 Middle Ground23 Race Rock24 Gills Rock25 Merrills Point26 Upper Gills Rock27 Great Slough Creek28 Morrill Creek29 Doles Island30 Cross Beach31 Simes Flats32 Crotch Creek33 Dock Creek

1 Common Island2 Hampton/Browns

River Confluence3 Browns River Area4 Middle Ground5 The Willows

Clam Beds

3132

3029

28

26

24 25

27

23

21

20

22

19

16

1518

17

14

13

129

8

6

57

11

4

310

2

1

FIGURE 3.4

Shellfish resources in theHampton Harbor Estuary.

tered, has been variable for the studyperiod, however, it can be stated thatdensity on all flats was highest from 1977through 1981, lowest from 1981 through1989, and although much lower than the1977-81 abundances, peaks in densityoccurred in 1990 and 1994. These peaksin density correspond well to the YOYdensities except for the years from 1983through 1987 where it appears that rea-sonably good sets did not survive thewinter (Figure 3.6).

Juveniles

Juvenile clams (26-50 mm), are morethan likely two year old clams. Theannual density of juveniles correspondswell with spat density with a one yearlag time. Clams of this size were mostabundant from 1979-1981, and havedeclined steadily since, though smallerpeak densities were recorded in 1990and 1995 (Figure 3.7).

Adults

Adult clams (>50 mm) were abundant in1971 through 1975 (Savage and Dunlop1983), declined from 1976-1979, and

reached peak abundances from 1980-1984. The steady sharp decline in abun-dance beginning in 1984 was very likelydue to heavy harvest pressure. A classicpredator prey relationship, where thechange in density of prey is tracked by achange in predator density (with somelag period), exists between the clampopulation and the number of adult clamlicenses sold (Figure 3.8). Closure of theflats in 1989 resulted in minor recoveryof adult clam density on the CommonIsland flat from 1989 to 1995, a muchgreater increase in density in clams onthe Seabrook flat, and little change onthe Hampton River confluence flat,though an increase was recorded from1994-1995. The Common Island flat wasreopened in 1994, however the effects ofrecreational clamming in 1994 and 1995appeared to have little effect on clamdensity (Figure 3.9). A recent studyfocused on removing blue mussels fromflats to improve clam habitats (Langanand Barnaby, 1998).

Predation, particularly of smallclams, can greatly affect the survival ofclams to harvestable size. The green

134

Seabrook Stationin Operation

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 1-5mm

Flat 1

Flat 2

Flat 4

FIGURE 3.5 Annual mean log10(x+1) density (number per ft2) of clams 1-5 mm length: 1974-1995. Data from NAI (1995)

135

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 6-25mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

Annual mean log10(x+1) density (number per ft2) of clams 6-25 mm length: 1974-1995. FIGURE 3.6Data from NAI (1995).

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams 26-50mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

Annual mean log10(x+1) density (number per ft2) of clams 26-50 mm length: 1974-1995. FIGURE 3.7Data from NAI (1995).

136

0

5000

10000

15000

Bushels

Licenses

1971 1973 1975 1977 1979 1981 1983 1985 1987

FIGURE 3.8 Number of clam licenses and the adult clam standing crop (bushels) in Hampton-Seabrook Harbor: 1971-1987. Data from NAI (1995).

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

Log10(x+1) Density of Clams >50mm

Flat 1

Flat 2

Flat 4

Seabrook Stationin Operation

FIGURE 3.9 Annual mean log10(x+1) density (number per ft2) of clams >50 mm length: 1974-1995. Data from NAI (1995).

137

crab, a major predator of Mya, has beenhighly variable over time in HamptonHarbor, but unlike human predators,their numbers are influenced by mini-mum winter water temperatures ratherthan prey (clam) abundance. Even inyears of low crab abundance, thereappears to be sufficient numbers of crabsin the Harbor to impact juvenile clamabundance. Other predators includenematodes, horseshoe crabs and birds.Though massive sets of clams could“breakthrough” and overwhelm preda-tion pressure, it is unlikely that this willhappen without substantial natural orartificial reseeding and predator protec-tion (Savage and Dunlop, 1983).

Ultimately, it appears that the con-trolling factors determining clam popula-tions in Hampton Harbor are larvalsettlement, predation, prevalence of sar-comatous neoplasia (Hampton River flat)and harvest pressure. Savage and Dun-lop (1983) stated that unless and seedclams are protected from predators andharvest pressure on adult clams is con-trolled, it would be very difficult for evenlarge sets of clams to overcome the rateof predation and produce increasedquantities of adult clams.

Softshell Clam Diseases: Sarcomatous neoplasia

Sarcomatous neoplasia, a lethal form ofleukemia in clams, has the potential tocause serious mortalities in the softshellclams. The infection has been observedin relatively pristine waters, however it issuspected that the rate of infection isenhanced by pollution.

Sarcomatous neoplasia was observedin Hampton Harbor clam populations inOctober, 1986 and February, 1987 fromthe Common Island (6%) and HamptonRiver confluence (27%) flats (NAI, 1996).No infections were found on theSeabrook flat (middle ground). Clam sur-veys in 1987 indicated that juvenile andadult densities were reduced by 50% inthe two flats where disease was identi-fied, while the population wasunchanged on the middle ground. It issuspected that the reduced densities

resulted from disease related mortalities.In November, 1989, twelve of fifteenclams (80%) from the Hampton Riverwere infected. From 1990-1995, adultclam densities quadrupled in the middleground, while Common Island densitiesdid not change, and Hampton River den-sity decreased by 50%. It is suspectedthat disease may have contributed to theobserved reductions. Clams in the GreatBay Estuary have not been examined forneoplasia.

Blue Mussels (Mytilis edulis)

The blue mussel is widely distributed inthe North Atlantic and occurs in Europeas well as North America. On the EastCoast of the U.S., it ranges from CapeHatteras to the Arctic Circle. Musselsinhabit the intertidal and subtidal zonesof estuaries and the open coast. Thoughprimarily a shallow water species, theyare sometimes found at considerabledepths. They can tolerate temperaturesranging from -2°C to 25°C and salinitiesranging from 5 ppt to 35 ppt, thoughprolonged expose to salinities below 15ppt are lethal. Spawning can occur yearround, though the peak spawning peri-od is June through August. Like otherbivalves, the larvae are planktonic andremain in the water column for three tofive weeks. Initial settlement occurs inshallow water on any firm substrate,however, newly attached juvenile mus-sels can detach their byssal threads anddrift with the currents in search of othersuitable attachment surfaces. Thoughmussels are harvested in large quantitiesand are an important aquaculturespecies in Europe, Canada and otherparts of the world, they are largelyignored as a food species in New Eng-land. They are considered by many tobe a nuisance species since colonizationleads to fouling of industrial and coastalstructures, as well as the hulls of ships.

Blue mussels can be found in theGreat Bay Estuary attached to any hardsubstrate in the intertidal and subtidalzones, and also colonize intertidal flats inscattered clumps and contiguous mats.Though during high salinity periods

mussels may be found in most areas ofthe estuary, their limited tolerance forlow salinity limits their permanentupstream distribution to the area aroundDover Point. Mussels are most abundantin the lower Piscataqua River, Ports-mouth Harbor and Little Harbor. Thelocation of some mussel beds in thelower estuary was identified as part ofthe Ecological Risk Assessment study forthe Portsmouth Naval Shipyard. Density,size and condition index of mussels froma number of sites was measured for thisstudy (Johnston et al., 1994). Banner andHayes (1996) mapped blue mussel habi-tat using a suitability index model, how-ever, the lower estuary where musselsare most abundant was not included intheir study.

Long term records of larval abun-dance and juvenile settlement of bluemussels have been maintained as part ofthe PSNH environmental studies pro-gram by Normandeau Associates (NAI,1996). Mussel larvae are a dominanttaxon in the nearshore plankton commu-nity and are the dominant noncolonialtaxon on shallow depth fouling panels.Density of larvae has increased in recentyears, and though settlement variesannually, in general it has increased inrecent years as well. Mussels can befound in the estuary attached to hardsubstrate in both the intertidal and subti-dal zones, and can form extensive bedson tidal flats. Banner and Hayes (1996)have mapped mussel habitat usingoccurrence and suitability indices. Themost prominent beds are located in theHampton River, Blackwater River, and onthe Seabrook middle ground clam flat.There is no scientifically documentedchange in abundance, though there isinformation (P. Tilton, personal commu-nication) that the coverage of mussels onthe Seabrook flat has increased in recentyears. Mussel density on the flats inSeabrook can be as high as 3500/m2

(Langan and Barnaby, 1998). Recentdevelopments in new culture techniques,combined with increased market valueand an abundant natural seed supplymakes this species an ideal candidate foraquaculture development.

Sea Scallops (Placopecten magellanicus)

Though primarily an oceanic species, seascallops can be found in the higher salin-ity areas of bays and estuaries in NewEngland below a depth of 5 meters. Sev-eral scallop beds are located in the lowerPiscataqua River and Portsmouth Harborand include the area between Salaman-der Point and Fort Point, in Spruce Creekand off Fort McClarey in Kittery, Maine.Langan (1994) examined the density, sizestructure and movements of scallops inthe Fort Point area using SCUBA surveysand mark and recapture studies. Meandensity was 1.3 scallops/m2 and with theexception of few small (10-20 mm) indi-viduals, the population had a normal dis-tribution. Small scallops are difficult tosee and may have been overlooked bydivers. Scallop movement is greater forthe 40-60 mm sized animals than smalleror larger individuals. Some large scallopswere found within 100 meters of therelease site a year after tagging. A projectwhich began in 1996 (Langan 1997) isinvestigating the spawning time, spatfalland growth and mortality of scallops insuspension and bottom culture. Thespawning period in 1996, based ongonadal/ somatic index (GSI), com-menced in late July and spat settlementbegan in October. Onion bag/monofila-ment type spat collectors were used tocapture larvae. Some collectors wereretrieved in March and scallops from 4-10 mm were retrieved. These scallopsand approximately one thousand 25 mmindividuals were placed in suspensionculture to measure growth and mortality.Natural enhancement of the bottomunder the collectors was assessed in thesummer of 1997.

Scallops are fished commercially withtowed dredges from November 1 to April14, and are harvested commercially andrecreationally using SCUBA. Other thanthe 1994 survey at Fort Point, there is lit-tle information on scallop density or pop-ulation change over time. Commercialfishermen indicate, however, that there isa great deal of variation in scallop abun-dance both temporally and spatially (P.Flanigan, personal communication).

138

139

Other Bivalve Species

Though there is no documented infor-mation on population densities andtrends, several other bivalve speciescommon to New Hampshire estuariesshould be mentioned. The deposit feed-ing clam Macoma balthica is common inall areas of Great Bay and Hampton Har-bor and the siphon of this clam is afavored prey item of juvenile winterflounder (Armstrong, 1996). Razor clams(Ensis directus) can be locally abundantin subtidal areas of Great Bay (Nelson,1981), and the ribbed mussel (Geukensiademissus) is also common in lower salin-ity and marsh areas of the Great Bay(Nelson, 1981) and Hampton/Seabrookestuaries. The gem clam, Gemmagemma, a very small bivalve, can be thedominant infaunal taxon in the sandierareas of Great Bay.

3.1.3.2 Crustaceans

American Lobsters

The American lobster is the largest crus-tacean inhabiting New Hampshire’s estu-aries and coastal zone. They are thetarget of a large and valuable commercialfishery which will be discussed in a latersection of this report. Though primarily acoastal and oceanic species, lobstersinhabit many coastal bays and estuaries.They range from the mid-Atlantic statesthrough Newfoundland, though in theirsouthern range, they are found in great-est abundance in deeper offshore waters.Though most often fished in shallowwaters (<100 ft), lobsters inhabit watersas deep as 1,500 ft. Lobsters are omnivo-rous, feeding on molluscs, urchins,starfish, crabs and even other lobsters.They in turn are preyed upon by seals,groundfish (cod) and other large preda-tory fish such as striped bass. The adultsundergo a seasonal migration, movinginshore in spring and offshore in the fall,though within that time period, they maymove about a great deal within estuaries(Dr. S. Jury, personal communication).Spawning occurs by means of internalfertilization when the female has recent-ly molted, and the fertilized eggs are

extruded one year after molting. Thefemales carry the fertilized eggs undertheir abdomen for up to one year. Theeggs hatch and are released into thewater column in late spring/early sum-mer in near shore areas, and the plank-tonic larvae go through several moltstages before settling to the bottom. Thepreferred juvenile settlement substrate isrock-cobble, (Wahle and Steneck 1991,1992) though older juveniles can befound inhabiting any type of substratewhere shelter (boulders, rocks, cobble,mud burrows) can be found. Lobstersreach commercial size after 15-20 moltsor in 6-9 years. Despite increased fishingpressure in recent years, lobster popula-tions are relatively stable. More informa-tion on lobster abundance is presentedin Chapter 4.

Crabs

Several species of crabs can be found inabundance in New Hampshire’s estuariesand coastal areas. Most prominent arethe rock crab (Cancer irroratus ) and thegreen crab (Carcinus maenas) thoughthe small mud crabs of the generaPanopeus and Rhythropanopeus are alsovery abundant. There is some commer-cial harvesting of rock crabs for humanconsumption and green crabs for bait,however, their economic importance isnegligible.

3.1.3.3 Horseshoe Crabs (Limulus polyphemus)

The horseshoe crab (Limulus polyphe-mus) is not a true crab, and among thearthropods is more closely related to thearachnids (spiders, scorpions) than crus-taceans. Horseshoe crabs are abundantin Great Bay and occur in lower numbersin Hampton Harbor. They are most con-spicuous in the month of June, whenthey mate in large numbers during thespring flood tides and deposit their eggson the beach. The eggs are preyed uponby several species of shore birds andrepresent a major food source for somespecies. Horseshoe crabs excavate largefeeding pits in soft substrates, consumingthe worms, molluscs and crustaceans.

Coastal New Hampshire and its estu-aries were well known for their vari-

ety and abundance of finfish species incolonial times. In fact, the area’s earliestsettlements were established in order toexploit the bountiful stocks of finfish.Throughout the eighteenth and nine-teenth centuries, overharvesting, the con-struction of tidal dams, destruction ofspawning grounds through sedimenta-tion and municipal and industrial pollu-tion greatly reduced their numbers in theGreat Bay Estuary (Jackson 1944). Asconditions improved toward the latterpart of this century, many species havere-established themselves since 1900.Today the Great Bay Estuary supports 52species of resident and migratory fish(Nelson, 1981) which are listed inAppendix E, while twenty eight specieswere reported for Hampton Harbor (NAI,1977). Estuarine species include yearround resident such as tomcod (Micro-gadus tomcod), mummichogs (Fundulussp.) and silversides (Menidia menidia),seasonal migrants such as bluefish(Pomatomus saltatrix) and striped bass(Morone saxatilis) and anadromous fishsuch as the river herrings (Alosa pseudo-harengus and A. aestevalis), shad (Alosasapisissima) and lampreys (Petromyzonmarinus) (Jackson, 1944; Nelson,1981,1982; Sale et al., 1992; Jury et al., 1994).Fishways constructed on the Cocheco(2), Exeter (2), Oyster, Winnicut andLamprey rivers in the Great Bay Estuaryhave enabled populations of severalanadromous species to rebound, howev-er, some species such as Atlantic salmon,and the common and shortnosed stur-geons (for which there is no reliable his-toric record of occurrence) and shadhave not successfully been reestablished,despite stocking efforts for Atlanticsalmon and shad. Commercially andrecreationally important species, includesmelt, (Osmerus mordax), winter floun-der, (Pleuronectes americanus), smoothflounder (Liopsetta putnami), and stripedbass, (Morone saxatilis). Finfish occur-rence, abundance and ecology havebeen studies by many groups including

the NH Fish and Game, NormandeauAssociates, Inc, the University of NewHampshire, U.S. Fish and Wildlife, andthe National Oceanic and AtmosphericAdministration (NOAA) as part of naturalresource inventories, impact assessmentsfor power plants and ecological researchprojects. Detailed information on estuar-ine and coastal finfish species can befound in Jackson (1994), Nelson (1981,1982), Sale et al. (1992), Jury et al.(1994), NAI (1977 and 1996) and fishhabitat has been mapped in G.I.S. formatby the U.S. Fish and Wildlife Gulf ofMaine Project (Banner and Hayes, 1996).Finfish research and monitoring by NHFish and Game, Normandeau Associatesthe University of New Hampshire contin-ues today, and provides updated infor-mation on finfish abundance. The statusand trends of finfish species selected fortheir commercial, recreational and eco-logical importance are described below.

3.2.1 SELECTED SPECIES

3.2.1.1 Striped Bass (Morone saxatilis)

As a result of the region-wide moratori-um and subsequent harvest restrictionson striped bass in the 1980’s and 1990’s,New Hampshire waters have experi-enced a tremendous increase in the sea-sonal occurrence of this species. Stripedbass abundance has increased steadilysince 1988. Though the data presented inFigure 3.10 are based on NH Fish andGame creel surveys and the size fre-quency of the fish are not noted, there isgeneral agreement among biologists andanglers that fish of all sizes haveincreased in abundance. Fish begin toarrive in mid to late May and remain inthe estuary until October. It is not knownif the same fish stay for the entire periodor of there is a continual immigrationand emigration of individuals during thisperiod. Catches of fish in the winter andearly spring indicate that some fish mayoverwinter in the Great Bay Estuary.Catches of legal (> 32”) and undersizedfish tagged by the U.S. Fish and Wildlife

140

3.2

ESTUARINE FINFISH

141

Winter FlounderCatch Per Trip

Striped Bass

19961988 1989 1990 1991 1992 1993 1994 19950

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

Catch per trip of striped bass and winter flounder. Based on survey information. FIGURE 3.10

1988 1989 1990 1991 1992 1993 1994 1995 1996

45

40

35

30

25

20

15

10

5

0

Kept

Released

Total Fish Caught

Striped bass caught in New Hampshire with U.S. Fish and Wildlife Service tags: 1988-96. FIGURE 3.11

Service have shown the same increasesince 1988 (Figure 3.11).

Detailed information on striped basspopulation status and trends for Hamp-ton Harbor is not available, though someof the data in Figures 3.5 and 3.6 wouldinclude fish captured in or near HamptonHarbor.

3.2.1.2 Winter Flounder (Pleuronectes americanus)

The recreational CPUE of winter flounderin Great Bay declined from 1988 to 1996,although CPUE was higher in 1995 and1996 than in 1994 (Figure 3.10). Similardeclines in abundance have beenobserved in Hampton Harbor. Largerindividuals of this species are not yearround estuarine residents and undertakeregular migrations out of the estuary inthe fall and return in the spring. Juvenilefish can be found in the estuary in allmonths, though their abundance is great-est from May through September. Winterflounder are subjected to very high fish-ing pressure in the nearshore (>3, <25miles) and offshore (>25 mi) waters andthe commercial CPUE in the Gulf ofMaine has declined dramatically since1982, after an increase from 1974 to 1982(NOAA 1992). Studies by Armstrong(1995) and Langan (1994, 1996) foundthat juvenile winter flounder are abun-dant in the estuary in spring and sum-mer, and forage in many differenthabitats. There is no clear preference forany one habitat and they can be found inthe intertidal zone at high tide as well asin channel bottom in deeper areas ofGreat Bay. Using an otter trawl Arm-strong (1995) averaged eight winterflounder per 10 minute tow in mid GreatBay from 1989 to 1992. Langan (1996),using the same type of fishing gear in thesame location averaged 7.9 flounder per10 minute tow in 1996. The size fre-quency distribution was similar for thetwo studies. Fish were collected in Sep-tember, 1991 (Johnston et al., 1993) andin the spring of 1993 (Langan 1994) inthe lower estuary as part of the Ecologi-cal Risk Assessment for the PortsmouthNaval Shipyard. In 1991, a series of fiveminutes tows yielded from 0 to 11 winter

flounder per five minute tow. Highestdensities were found in the Clark Islandembayment and near Fishing Island.Mean length frequency varied by station,ranging from < 100 mm to nearly 300mm. Trawls and seine hauls in 1993 atsimilar stations yielded up to fifty smallflounder per seine haul in shallow waternear Fishing island, the Kittery backchannel, Clark Island embayment andthe Police Dock area of Seavey Island.The mean size of fish captured in seinehauls was 57 mm. Larger fish were cap-tured with an otter trawl in the backchannel and Clark Island Embayment. Atotal of 48 fish were captured in 10 fiveminute tows, with a mean size of 366mm.

Though juvenile fish appear to beabundant in the estuary, the recreationalangler CPUE has declined in recentyears. This is no doubt attributable tostock depletion from heavy commercialharvest pressure in the Gulf of Maine.

Catches of winter flounder at threestations in the Hampton/Seabrook Estu-ary have declined since 1980, thoughthey have remained somewhat stablesince 1987. The reason for the decline isattributable to overexploitation by com-mercial fishing in the Gulf of Maine (NAI,1996)

3.2.1.3 Rainbow Smelt (Osmerus mordax)

The rainbow smelt is a common speciesin the Great Bay Estuary and is fishedthrough the ice by commercial and recre-ational fishermen in the winter. They arean anadromous species that enter theestuary in fall and winter and ascend thetidal rivers in the Great Bay Estuary afterice-out to spawn. Based on angler CPUE,the abundance of smelt has been highlyvariable from 1987 to 1996 (Figure 3.12).CPUE reached a low point in 1992 andincreased from 1993-1996. Average smeltegg deposition measured in the uppertidal reaches of the rivers from 1979through 1996 has also been highly vari-able. Predation by striped bass mayaffect smelt populations.

Rainbow smelt abundance has beenmonitored by seine hauls at three sites in

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Hampton Harbor. Though abundancehas been variable for the 19 year period(1976-1995), there is no discernibletrend. The greatest abundances wasmeasured in 1990, 1979, 1984, 1993 and1994, and lowest abundances in 1978,1980, 1992 and 1995.

3.2.1.4 River Herring: Alewife (Alosa pseudoharengus) and Blueback (Alosa aestovalis)

River herring (two species) are anadro-mous fish that migrate into the Great BayEstuary in the spring and ascend thebay’s tributaries to spawn. Though damsprevented these fish from reaching thefreshwater portions of the rivers formany years, the construction of fishwaysin the 1970s has enabled passage of thefish to freshwater.

The NH Fish and Game has moni-tored spring returns of river herring at

fishways in the Cocheco, Exeter, Lam-prey, Oyster and Taylor (Hampton Har-bor) rivers since 1975. Returns to theExeter, Lamprey and Taylor rivers show adecline in numbers, while the Cochecoand Oyster rivers show an increase (Fig-ure 3.13). The most dramatic decline hasbeen in the Taylor River. The reason forthe declines in some rivers is unknown,though predation by striped bass andchanges in water flow may be factors.This species is also fished commerciallyfor bait by offshore and inshore gillnet-ters. Records for catches by holders ofinland netters permits are available.

3.2.1.5 American Shad (Alosa sapidissima)

Spawning adult American shad havebeen stocked from 1980 to 1995 in theLamprey and Exeter rivers, and from1980-1988 in the Cocheco and Lamprey

16

14

12

10

8

6

4

2

01987 1988 1989 1990 1991 1992 1993 1994 1995 1996

Squamscott RiverBellamy/Oyster River

Lamprey RiverGreat Bay

Smelt CPUE (#/Angler Hour)

Smelt CPUE by area (number caught per angler hour): 1987-1996. FIGURE 3.12

rivers. Numbers stocked in the ExeterRiver increased each year since 1980,however this has not been reflected inthe number of returning fish (Figure3.14). A large number of fish returned tothe Lamprey River in 1988, however fewhave returned since. The best ratio ofreturning to stocked fish has been real-ized for the Cocheco River, where thefewest adult fish were stocked. It may bepossible that returning shad are inter-cepted by commercial gillnetters in theGulf of Maine. Though the flesh is gen-erally not consumed, the roe are consid-ered a delicacy. The springtime harvestof shad in local offshore waters may beaffecting the returns.

3.2.1.6 Atlantic Silversides (Menidia menidia)

Silversides are a small, short-lived, andhighly abundant estuarine species thatare found in both Great Bay and Hamp-ton Harbor. They generally inhabit shal-low waters and are an important preyspecies for larger predatory fish. In the1980-81 Fish and Game surveys (Nelson,1982), they were the most abundant fish

species captured in shallow waters andoften represented >50% of the total catch.Young striped bass (12-24") have beenobserved to feed heavily on silversides inthe Great Bay Estuary. The abundance ofsilversides has not been moni- tored inrecent years, therefore it is not possible todetermine trends in abundance.

The abundance of Atlantic silver-sides has been monitored by seining atthree stations in Hampton Harbor from1976 to 1995, though the years 1984-1987were not sampled (NAI, 1996). A declinein abundance beginning in 1982 from thepeak abundances during the period1976-1981 was observed. Since 1982, thepopulation has shown some interannualvariation, but appears to have changedlittle to the present (Figure 3.15).

3.2.1.7 Atlantic Salmon (Salmo salar)

Although once abundant, the anadro-mous Atlantic salmon is uncommon incoastal New Hampshire, except as astocked species. Overexploitation, thedestruction of spawning grounds by saw-dust and sediments in the 1800s, and

144

1975 1980 1985 1990 1995

450,000

400,000

350,000

300,000

250,000

200,000

150,000

100,000

50,000

0

Cocheco

Exeter

Lamprey

Taylor

Oyster

FIGURE 3.13 River herring returns in Seacoast rivers: 1975-1996.

145

1980 1982 1984 1986 1988 1990 1992 1994 1996

1600

1400

1200

1000

800

600

400

200

0

Exeter

Lamprey

Cocheco

Number of spawning adult American shad stocked in the coastal rivers of New Hampshire: 1980-1996. FIGURE 3.14

Mean Catch per Unit Effort

0.0

0.2

0.4

0.6

0.8

2.0

1.8

1.6

1.4

1.2

1.0

1975 1980 1985 1990 1995

NotSampled

S1S2S3Mean

Seabrook Stationin Operation

Annual geometric mean catch of Atlantic silversides per unit effort in Hampton Harbor in seine FIGURE 3.15samples (number per haul) for three stations and the combined mean of all stations: 1976-1995.

dam construction resulted in the cessa-tion of any natural runs of Atlanticsalmon. The decline in Atlantic salmonpopulations is regional rather than local,and only a few native spawning runsremain in some Maine rivers. Atlanticsalmon alevins have been stocked intributaries to Great Bay since 1989, andsome adults have been stocked in recentyears. However the success of the pro-gram is yet to be determined.

3.2.2 Fish Kills

In the past several years three incidentsof fish kills have been reported in theGreat Bay Estuary, all involving alewives(Alosa pseudoharengus). In 1993, aschool of alewives ascended a temporaryspillway created by a pond draw downfrom the Exeter Water Works. The fishascended the spillway to the pond fromwhich there was no means of escape.The fish depleted the oxygen in the pooland 375-450 fish died as a result. Mr. Vir-gil Harris of the Exeter Water Departmentreported that similar incidents have

occurred over the past twelve years dueto pond draw downs. The NH Fish andGame Department recommended alter-ing the draw down schedule to avoidsubsequent alewife strandings.

The second incident occurred in thefall of 1995 when a private citizen report-ed approximately 100 dead alewivesnear Bay Ridge Road in Greenland. Thecause of death was not identified, how-ever, it was speculated that a short termstress from a drop in salinity caused byhigh freshwater inflow during the periodor an isolated low dissolved oxygen con-dition caused the fish kill.

In October of 1997, nearly 2,400juvenile alewives which were migratingfrom fresh to tidal waters were killedover a two day period by physical trau-ma caused by an hydroelectric turbine atthe Cocheco River dam in downtownDover. New Hampshire Fish and Gamepersonnel reported that the mechanismthat allows the fish to bypass the turbinewas not operating properly. Correctiveactions were initiated.

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3.3.1 STATUS AND TRENDS OF SALT MARSH

Salt marshes are specialized habitatscharacterized by emergent vascularplants that extend within the intertidalzone from approximately mid tide heightto just above the elevation of the normalspring tide line. The total area of tidalmarshes within the entire state has beenestimated at 7,500 acres in 1974 (3,040ha; Breeding et al., 1974) and at 6,200acres in 1994 (2,500 ha; USDA, 1994).The difference may not indicate an actu-al decline, since no significant losses inmarsh acreage have been documented inten years of 305b reports issued by NHDES. The ecology of salt marshes of theGreat Bay Estuary has been reviewed byShort and Mathieson (1992), and plantspecies occurring in the salt marshes ofNew Hampshire have been listed in this(Appendix J) and earlier reports (NAI,1988; Ward et al., 1993). The most com-mon plant associated with the low marshin New Hampshire is the tall form ofSpartina alterniflora (salt marsh cord-grass); the most common high marshspecies include Spartina patens (saltmeadow cordgrass), the short form ofSpartina alterniflora, Distichlis spicata(spike grass) and Juncus gerardii (blackgrass) (USDA, 1994). In addition, there isa list of all plant species that occur inNew Hampshire wetlands (Reed, 1988).

3.3.1.1 Distribution, Standing Crop and Productivity

Salt marshes were identified and mappedfor the National Wetlands Inventory(Tiner, 1984) and more recently in twostudies that covered the tidal marshes ofthe state (NAI, 1988, Ward et al., 1993).No comparison of the inventories hasbeen made, but the more recent work ismore accurate and differences, if deter-mined, may not actually reflect changesin salt marsh distribution. The tidalmarshes within the Great Bay Estuary,including all tributaries, were mappedutilizing color infrared transparenciesand extensive ground truth work (Ward

et al., 1993). Based on this work, thelocation and areas of salt marshes andalgal beds in the Great Bay Estuary werecalculated by Weiss (1993). A total of2,230 acres (9.025 km2) of tidal marshare located in the Great Bay Estuary, withthe lower Piscataqua River, the Squam-scott River, and the Great Bay having themost extensive tidal marsh area. Coupledwith the National Wetlands Inventorymap, the Great Bay data provided thebasis for another salt marsh map pro-duced by USF&WS (Figure 3.16; Bannerand Hayes, 1996).

Annual aboveground productivity ofsmooth cordgrass (Spartina alterniflora)was estimated by Chock (1975) to beapproximately 604 g dry weight/m2/yrfor a salt marsh at Cedar Point (LittleBay). No estimates of total annual pro-ductivity (including belowground pro-duction) have been reported for saltmarshes in New Hampshire. However,some standing crop data, usually sam-pled during peak aerial biomass or at theend of the growing season, are available.Standing crop does not include theleaves and shoots produced that wereeaten, dead, or otherwise removed overthe course of the year. Peak standingcrop measurements for high marshesdominated by salt meadow hay (Sparti-na patens) as well as low marsh areas ofS. alterniflora are found in Table 3.5 andin the following references (Nelson,1981; Short, 1987; Short and Mathieson,1992; Burdick, 1992; Burdick andDionne, 1994). In an examination of therelationship between above and below-ground standing crop, Gross et al. (1991)report values for a high marsh dominat-ed by short form S. alterniflora in Rye of527 and 754 g dry wt/m2 of total aboveground and live below ground standingcrop, respectively.

Although often ignored, salt marsh-es can contain a significant macroalgalcomponent. This is especially true oflow marshes dominated by S. alterniflo-ra occurring near extensive intertidalmacroalgal beds (e.g., Little Harbor,Cutts Cove) where they may become

3.3

MARINE PLANT HABITATS:

Salt Marshes,Macroalgal Beds

and Eelgrass Meadows

Site [Years of data] Habitat (n/yr) S. alterniflora S. patens Other* Algae Total

Little Harbour1 [1] Low marsh (6) 512 0 0 1020 1532High Marsh (6) 28 614 12 3 657

North Mill Pond2 [3] Low marsh ( 8) 683 ** 14 9 70

Cutts Cove2 [3] Low marsh (16) 322 ** 35 818 117

Great Bay NERR3 [1] High marsh (5) 56 311 22 0 38

Rye Harbor3 [1] High marsh (5) 50 293 12 0 35

*Other vascular plants, including grasses and fortes, e.g., Salicornia europaea. ** Spartina patens was the predominant species in this category, but was lumped with Other. 1 = Burdick 1994, 2 = Burdick and Short 1997, 3 = Burdick, unpublished data

Standing crop of peak aboveground plant biomass in New Hampshire salt marshes (biomass = g dry wt/m2).

heavily colonized by fucoid algae withdistinctive growth forms, called marshecads (Ascophyllum nodosum varietyscorpioides and Fucus vesiculosus vari-ety spiralis; Norton and Mathieson,1983). In a study of seasonal trends inthe standing crop of S. alterniflora, theassociated ecads of fucoid algae werealso assessed by Chock (1975), whoconcluded they contributed greatly tomarsh productivity. A later study ofeight coastal salt marshes near themouth of the Piscataqua River foundfucoid biomass ranged from 100 to over1300 g dry weight per m2 with the algaeaveraging almost 60% of the total plantbiomass found in the low marshes (Bur-dick, 1994).

3.3.1.2 Habitat Impacts and Losses

Threats to salt marshes in New Hamp-shire have been reviewed and summa-rized (USDA, 1994). Specific threats andimpacts to marshes were categorized byhuman activities that are considered tobe important. Currently, marine develop-ment poses the greatest threat to saltmarshes through dredging, dock con-struction, shoreline development alongthe upper marsh edge, and developmentacross marshes that result in tidal restric-tions. Other potentially importantimpacts to marsh function include har-vesting marsh resources and conflictinguses within these habitats.

Dredging Impacts and Harvesting Effects

Dredge and fill operations have alteredmarshes within all of the seacoast estuar-ies to some extent. Large areas of theHampton-Seabrook marsh were dredgedand filled for residential housing. RyeHarbor has been dredged on severaloccasions, and in 1941 and 1962 thespoil was placed on the salt marsh land-ward of the harbor. This transformedseveral acres of marsh into upland habi-tat and has negatively impacted over 10additional acres. The ecological impactsat the sites of sediment dredging havenot been assessed, but impacts to themarsh from disposal were reviewed byBurdick (1992). Elevating the surface andsurrounding the area with earthen dikesseverely reduced salt water flooding andincreased fresh water flooding in thespring. These changes lowered soil salin-ity, led to the displacement of nativemarsh plants by Phragmites, Typha andupland plants, resulted in the formationof die-back areas and large pools ofwater, and caused a direct loss of fishhabitat.

In addition to direct negativeimpacts, dredging may reduce sedimentsources to marshes, leading to an inade-quate sediment supply to support marshmaintenance and development. Dredg-ing may also increase the wave energyenvironment, leading to increased ero-

148

TABLE 3.5

149

FIGURE 3.16

Habitat map for cordgrass/salt hay.

From Banner and Hayes (1996).

Cordgrass/Salt Hay Habitat

sion at the seaward edge of marshes. Onthe other hand, increased sediment sup-ply or a reduced wave environment fromdredging may allow the expansion of amarsh at its seaward edge.

Although salt hay was harvestedwidely along the New Hampshire sea-coast from the 17th to 20th centuries, theintensity of marsh management toimprove yields and harvesting efficiencyare poorly known (Breeding et al., 1974).Ditching to improve hay yields (notequivalent to mosquito ditching) was rou-tine. Salt hay farming continues to this dayand has experienced a small revival innorthern Massachusetts, yet the impactsfrom salt hay farming on salt marshecosystems are unknown (Rozsa, 1995).

Impacts from Docks, Piers and Shoreline Development

Impacts from docks and piers on saltmarshes have not been assessed in NewHampshire. Clearly, solid fill and cribstructures built on marshes eliminatesthem and are discouraged, but openpiers have also been shown to reduceproductivity and viability of salt marshesin other New England States (MichaelLudwig, NMFS Milford, CT). The USACOE has issued design guidelines forstructures over marshes (height over sed-iment needs to be at least as great aswidth of the structure), but it is not clearwhether such guidelines prevent degra-dation, nor have the dock impacts tomarshes been assessed quantitativelyand systematically.

Similar to docks, impacts from otherforms of shoreline development aresevere when structures are built uponand over marshes. However, structuresplaced at the landward edge of saltmarshes can also have serious effects onmarsh viability and maintaining thesehabitats in the near future (Pethick,1983). Because sea level is rising, andmarshes have traditionally migrated land-ward as well as built vertically to main-tain themselves in the face of rising sealevel (Redfield, 1965), increased local sealevel is expected to be accompanied bylandward migration of salt marshes.However, structures placed at the land-

ward edge of salt marshes will preventthese habitats from migrating landwardwith local sea level rise (Pethick, 1983).Furthermore, the rate of sea level rise isexpected to increase in New Hampshirefrom 1.2 to 7.5 mm/year. Structures thatprevent marshes from migrating land-ward will result in marshes becomingnarrow and lower in elevation. In time,waves reflecting from submergingmarshes will erode the marsh peat andexacerbate local erosion and floodingproblems (Smith et al., 1978).

Impacts from Tidal Restrictions

Tidal restrictions influencing estuarinecirculation and other functions relating towater quality that have been caused byroads, railways, dikes and causewayshave severe long-term impacts to saltmarshes. Construction in the intertidaland subtidal areas of an estuary alwaysinfluences circulation patterns to someextent (Miller and Valle-Levinson, 1996),but linear features built on or along saltmarshes that restrict tidal flow have sig-nificant impacts (Marrone, 1990). Besidesaltering circulation, these structuresreduce flooding by salt water and tend toretain fresh water (especially in thespring), and can ultimately result in anon-tidal freshwater marsh.

Restrictions to tidal flow in saltmarshes lead to areal (if habitat becomesnon-tidal) as well as functional losses. InNew Hampshire, significant tidal restric-tions have been fully documented(USDA, 1994) and there are indicationsthat some marshes are deteriorating.Deterioration includes replacement ofemergent salt marsh vegetation by openwater, unvegetated flats, freshwater plantspecies or invasive species such as purpleloosestrife and common reed. Marshdeterioration is a symptom of changes inlocal processes with the result that themarsh is unable to maintain itself. Besidesreducing or even excluding fish access totheir habitat (Burdick et al., 1997), tidalrestrictions appear to lead to declines inproductivity and habitat value for wildlife.

Impacts to water quality and soilchemistry from tidal restrictions are notwell known, but serious negative

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151

impacts to water quality have been doc-umented elsewhere (Portnoy, 1991). InNew Hampshire, current knowledge islimited to soil and creek salinity, soilredox potential, soil moisture and soilorganic matter (Short, 1984; Burdick,1992; Burdick and Dionne, 1994;Ammann unpublished data; Burdick etal., 1997; unpublished data).

Salinity changes are the most obvi-ous impacts, with restrictions generallyleading to freshening of the marsheswhen compared to control marshes orthe same marshes following restorationof tidal exchange (Table 3.6). Reductionsin salt water flooding to restricted marsh-es allows for chemical and microbial oxi-dation of reduced soil constituents,leading to higher, more positive redoxpotentials, loss of soil organic matter, andlower pH (Burdick and Dionne, 1994).Furthermore, the ability of the marshes toremove suspended sediments from tidalwaters is certainly curtailed by tidalrestrictions, though these impacts fromrestrictions have not yet been quantified.

3.3.1.3 Habitat Change Analysis and Modeling

Large areas of salt marsh have been filledfor residential and industrial develop-ment (Breeding et al., 1974) while otherareas are deteriorating due to tidalrestrictions commonly associated withroads. It is estimated that New Hamp-shire still has 50% of its 18th Century tidalwetlands and 90% of its 18th Centurynon-tidal wetlands (NHDES, 1996b).More recent data summarizing impacts ofpermitted projects and known violationson tidal and non-tidal wetlands are con-tained in the bi-annual 305(b) reportssent to Congress by NHDES. There hasbeen very little net loss of tidal wetlandsin the past 10 years (Table 3.7). The dataindicate small losses have occurred innon-tidal wetland acreage statewide,although the most recent report statesthat “...there has been no measurable netloss of wetlands functional value”(NHDES, 1996b). Natural gains in wet-lands through the activities of beaver asthey dam creeks and flood forests is esti-

Soil SalinityBefore After After Reference

Estuary/Marsh name Type of Restriction Restriction Restriction Restoration marsh

Hampton EstuaryDrakeside Rd Marsh1 Undersized Culvert — 8.5 10.1 10.5

Rye HarborAwcomin Marsh2 Diked dredge fill — 6.5 21.6 24Locke Road Marsh3 Undersized Culvert — 16.4-27.0 NA 23.1

Great Bay EstuaryPeverly Ponds4 Causeway with Tidal Gate — NA NA(GBNWR)Sandy Point Marsh1 Berm formed by debris — 5.6 25.1 25.2(GBNERR)Mill Brook Marsh5 Causeway with Tidal Gate — 0.0 19.5 16.2(Stuart Farm)

Approximately 50 other sites in New Hampshire are hydraulically restricted as determined by the NRCS (USDA 1994), but no data on soil chemistry at other sites is available at this time.

1 Burdick, Unpublished data2 Burdick and Dionne, 19943 Little, Unpublished data4 USF&W Service, Data unavailable at this time5 Burdick et al. 1997

Soil salinity changes in salt marshes from hydologic manipulations. TABLE 3.6

mated to be in the tens of acres eachyear (NHDES, 1989a).

Specific restrictions causing deterio-ration of the salt marshes have been enu-merated for the tidal wetlands of NewHampshire by the Natural Resource Con-servation Service (USDA, 1994). Theyfound 50 tidal restrictions in the statewhich encompass over 20% of the saltmarsh area remaining in NH (1,300 outof 6,200 acres; USDA, 1994). The reportshows that marshes deteriorating fromtidal restrictions are more commonlyfound at the upland borders of largemarsh systems (i.e., Hampton/SeabrookEstuary) and behind smaller barrierbeach systems (i.e., Little River Marsh),but are spread throughout the state. Asdiscussed previously, deteriorationincludes losses in salt marsh acreage aswell as functional losses. Thus in contrastto the 305(b) reports (NHDES, 1996b), itappears that indirect losses of tidal wet-land acreage as well as functions contin-ue to occur. However, restoration of tidalexchange to some sites may be able toreverse some of these wetland losses(see restoration section).

Preliminary results of change analy-ses based on aerial photography ofselected marshes in the tidal reaches ofthe Squamscott River indicated someincrease in open water (salt pannes) inseveral marshes (Ward, in preparation).

The development and evolution ofsalt marshes in New Hampshire isthought to follow the widely held modeldeveloped in Massachusetts by Redfieldin 1965, later verified by Keene (1980) ina Hampton marsh, and recently verifiedand modified for salt marshes in Maine

by Kelley et al. (1995). Modern marshesbegan developing about 4,000 years agowhen sea level rise slowed and lowmarshes became established on intertidalsediments. The low marshes expandedseaward and at the same time collectedsediments to build vertically and becomehigh marsh. The high marsh, in turn,expanded seaward following the expan-sion of low marsh and landward cover-ing upland as sea level slowly continuedto rise, resulting in the flat, high marshhabitat that is typical of New Hampshiresalt marshes.

A conceptual model of the changesin marshes due to impacts from tidalrestrictions has recently been proposedby Burdick et al. (1997), but estimationof rates within the model for simulatingchanges in tidally-restricted and restoredmarshes have not been made or verified.Furthermore, few of the marsh functionsthat are responsible for socially-esteemedvalues have been quantified. Increases inour understanding of habitat functionsand change will support modeling andimprove marsh management.

3.3.2 STATUS AND TRENDS OF MACROALGAE

3.3.2.1 Distribution, Standing Crop and Productivity

Macroalgal habitats are best character-ized as those where seaweeds are foundgrowing on rocky shorelines and into thesubtidal zone to depths where the sea-weeds, being light dependent, remain inthe photic zone. Seaweeds also formimportant ecological components of saltmarshes, seagrass beds, mudflats, chan-

152

Tidal Wetlands (acres) Non-tidal Wetlands (acres)Year Impacted Total Impacted Total

1987-88 0 7,500 25-50 95,0001989-90 0 7,500 50 200,0001991-92 0 7,500 150 192,5001993-94 0 7,500 200-300 400,000-600,0001995-96 0 7,500 150-250 400,000-600,000

Impacts of permitted projects and known violations on state-wide wetlands: 1988-1996. Datafrom NHDES (1996).

TABLE 3.7

153

nels, and artificial substrata such as pil-ings and rip-rap, but the focus in thisreport is on the rocky shorelines andchannels dominated by seaweeds. Thereare a total of 219 seaweed speciesknown from New Hampshire (AppendixJ; Mathieson and Hehre, 1986; Mathiesonand Penniman, 1991). In these reports,large-scale spatial and seasonal distribu-tions are reported for many algal speciesand the factors that control the distribu-tions are discussed. For example, somespecies were found to occur in Great Baybut not on the open Atlantic Ocean. Dis-tribution maps showing species occur-rences at specific sites were compiledfrom these earlier works by Banner andHayes (1996) for knotted wrack (Asco-phyllum nodosum), Irish moss (Chon-drus crispus) and tufted red weed(Macrocarpus stellatus) (Figures 3.17;Banner and Hayes, 1996). At specificsites, changes in algal communities havebeen documented (e.g., Dover Point byReynolds and Mathieson, 1975), and thepotential for revisiting other previouslysampled sites is very good. However,long term changes in algal distributionsover time are not currently available.

A detailed study of the occurrenceand standing crop of algal species alongthe shores of the Oyster River and itstributaries was conducted in 1993 (Math-ieson, unpublished data). Enteromorphaprolifera, Ulva lactuca, Ascophyllumnodosum and Fucus vesiculosus werecommon to virtually all areas. The occur-rance of Polysiphonia harveyi, Ulvaoxysperma, Chondrus crispus, Gracilariatikvahiae and unidentified cyanobacteriawere also measured in a few tributaries.The location of the algae with respect toelevation within the intertidal zone wasalso noted.

Standing crop and growth estimateshave been made for a few species of redand brown algae and these reports char-acterize the habitats as well (Mathiesonand Burns 1975; Chock and Mathieson1976; Mathieson et al. 1976; Josselyn andMathieson, 1978). In 1993, a minor sur-vey of algal species that estimated stand-ing crop by species was conducted byMathieson at Adams Point and reported

in Langan and Jones (1993). Paired repli-cate clip plots at top, middle, and lowerintertidal zones showed the dominanceof the brown fucoid algae, Ascophyllumnodosum, with important contributionsin the middle and lower zones by bothred and green species.

3.3.2.2 Habitat Impacts and Losses

Channel work in the lower PiscataquaRiver has occurred on many occasions,and included blasting ledges, dredging inthe river, as well as in Little Harbor at theturn of the century. Few studies are avail-able that document impacts to intertidaland subtidal plant habitats, and impactsto benthic communities have beenregarded as minor in the past (i.e.,Brown and Fleming 1989). Dredging notonly directly removes algal habitat, itreduces algal production and survivalbecause suspended sediments from thedredging attenuates light needed forgrowth. Furthermore, the hard clean sur-faces needed as sporelings attachmentpoints become unsuitable for macroalgalrecruitment after dredging activitiescover them with fine sediments.

Shoreline development typicallyremoves or buries algal beds in the inter-tidal zone. The extent of these impactsalong our coasts has not been deter-mined. However, placement of hard sur-faces at these sites can often lead to newalgal beds if algae can colonize the newsurfaces (e.g., bridge abutments, rip-rapwalls).

Algae has been harvested for varioususes in New England, but such harvest inNew Hampshire estuaries is poorlyknown and probably minimal. Algin andcarrageenan are extracted from kelps,knotted wrack (Ascophyllum nodosum)and Irish moss (Chondrus crispus) andare used as additives in the food indus-try. Few algae are consumed directly inthis country, but dulse (Rhodymeniapalmata) and nori (Porphyra sp.) are har-vested for consumption. Knotted wrackis also used for packing material to pre-serve live shellfish and worms. Impactsto the algal resources from experimentalharvesting have been assessed for thered algae Irish moss (Mathieson and

154

Tufted Redweed

Rockweed

Irish Moss

OccurancesFIGURE 3.17

Habitat map for rockweed, Irish moss and tufted redweed. From Banner and Hayes (1996).

155

Burns 1975). They found that plantscould recover in a year after carefullycontrolled harvesting, but winter harvest-ing had greater impacts and overharvest-ing could cause demise of the algal beds.

3.3.2.3 Habitat Change Analysis and Modeling

What little is known about habitatchange regarding the macroalgal bedsof New Hampshire estuaries includesstudies on the destruction of estuarineand near shore populations of kelp by asmall species of estuarine snail, Lacunavincta (Fralick et al., 1974). The stand-ing crop and assemblage of algalspecies may be used as an indicator ofnutrient status of specific sections ofestuaries. Nutrient poor areas supportslow-growing long-lived species where-as over-enriched areas become lessdiverse and dominated by opportunisticspecies indicative of poor habitat health.Although no synthesis currently exists,analysis of existing data and revisitingsites sampled 20 years ago could pro-vide interesting information on the sta-tus and trends of estuarine health inNew Hampshire.

The use of models to describechanges in algal beds has received littleattention. In 1978, Josselyn and Math-ieson (1978) created a model todescribe seasonal changes in living bio-mass, dead biomass found on the strandline as wrack, and decomposition ofwrack for fucoid algae and eelgrasswithin Great and Little Bays.

3.3.3 STATUS AND TRENDS OF EELGRASS BEDS

Eelgrass habitat provides the largest spa-tial distribution of any habitat withinGreat Bay (Short et al., 1992; Short andMathieson, 1992). Eelgrass beds in theestuary occur as large meadows andsmall contiguous beds forming intertidaland subtidal seagrass habitats. Eelgrasshabitat functions as breeding and nurs-ery grounds for the reproduction of fin-fish, shellfish, and other invertebrates.Eelgrass meadows serve as a feedingarea for many fish, invertebrates and

birds. Additionally, eelgrass may act as afilter of nutrients, suspended sediments,and contaminants to the waters of theestuary.

3.3.3.1 Distribution, Standing Crop and Productivity

Distribution maps of eelgrass are avail-able for most of the Great Bay Estuaryfor the mid-1980s (Short et al., 1986) forGreat and Little bays through the 1990s(Short, unpublished) and for the mouthof Little Harbor in 1996 (Short, 1996).Most eelgrass habitat in New Hampshirehas been surveyed within the last sixyears; however, a comprehensive map ofthese findings has not been compiled. AGIS layer of eelgrass habitat has recentlybeen completed by the U.S. Fish andWildlife Gulf of Maine Project (Bannerand Hayes, 1996).

Eelgrass in the Great Bay Estuary hasexperienced fairly dramatic changes inpopulation distribution and total produc-tivity over the last two decades. Spatialand temporal changes in eelgrass popu-lations prior to 1991 have been reportedin numerous publications (Short et al.,1986; Short and Mathieson, 1992; Short etal., 1992; Short et al., 1993; Burdick andShort, 1995) and these data are shown inFigure 3.18. The Great Bay Estuary suf-fered from a decline in eelgrass popula-tions during the 1980s resulting in a lowpoint of eelgrass distribution in 1989.These decreases in population representdramatic losses of eelgrass habitat as aresult of wasting disease (Short andMathieson, 1992). Similar problems andtrends in eelgrass populations have beenreported for the neighboring AnnisquamEstuary at Cape Ann in Massachusetts(Dexter, 1985). The period of eelgrassdecline in Great Bay was followed byrapid recovery where extensive seedproduction led to extensive revegetationwithin Great Bay proper. This recoverycan be seen by comparing Figures 3.19and 3.20. In contrast, some beds in LittleBay and along the Piscataqua River havenot reappeared and efforts are underwayto protect remaining beds from develop-ment and restore significant beds tothese portions of the estuary.

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FIGURE 3.18 Time series of eelgrass distribution in Great Bay.

July 1989

August 1987

July 1988

September 1990

September 1991

September 1992

Standing crop and other populationcharacteristics of the eelgrass populationnear the red nun buoy at the mouth ofGreat Bay were made in 1987, 1989 and1993 (Table 3.8; Langan and Jones,1993). Both shoot and total (shoots, rootsand rhizomes) standing crop data showincreases between 1987 and 1993, theperiod when eelgrass was declining andthen recovering from episodes of wast-ing disease. The Wasting Disease Indexwas measured for each year and showed

the greatest levels of disease occurred in1989, the year that most of the beds inGreat Bay had succumbed to the disease(Short et al., 1993).

3.3.3.2 Habitat Impacts and Losses

Dredging Impacts on Benthic Habitats and Sediments

As previously mentioned, creation andmaintenance of navigable channels inthe Great Bay Estuary has occurred for

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many years, though little informationexists that describes impacts to eelgrassbeds. In 1992, the threat to an eelgrassbed from dredging and constructing thenew Port of New Hampshire pier facilitywas recognized as a serious ecologicalimpact which required habitat mitigation.As a result, seven acres of eelgrass weretransplanted into various sites within theestuary. A proposed dredging at themouth of Little Harbor to deepen moor-ing areas may impact some of the twen-ty five acres of eelgrass beds.

Impacts of Boating, Docks, and Piers

In general, commercial boat operatorshave had little impact on submerged haz-ards, including submerged vegetation.However, recreational boaters are oftenunfamiliar with such hazards and haveoften been observed entangled in eel-grass or grounded on the shallow flats ofeelgrass beds in Great Bay (Burdick, per-sonal observation). Further evidence ofboat damage in Great Bay includes boatscarring from propellers and damagefrom hulls during groundings, but thedamage appears to be minor and thebeds have rapidly revegetated (Burdick,personal observation). Continued recre-ational boat use in the estuary will posecontinued risks to eelgrass meadows.

Because docks and piers cross shal-low subtidal habitats to secure vessels indeeper waters, it is likely that these struc-tures have crossed and impacted eelgrassbeds and other habitats (Burdick andShort, 1995). However, no recordremains for whatever impacts haveoccurred over the past three centuriesfrom these structures. Currently, few

docks appear to influence eelgrass beds.The large commercial dock being builtfor the expansion of the Port of NewHampshire will have significant impacts(see habitat mitigation section below)that is being assessed.

Impacts from Shoreline Development and Harvesting

Human development of the shorelinearound Portsmouth Harbor, including thePortsmouth Naval Shipyard, has filledmany acres of shallow estuarine habitatthat was at least partly occupied by sea-grass beds and salt marshes. Specificinstances include the expansion of theShipyard in the 20th century which con-nected several islands and most recentlyincluded filling marshes and mudflats forthe Jamaica Island Landfill in the 1970s(Johnston et al., 1994). Similarly, devel-opment of transportation and marinefacilities around Noble’s Island resultedin filling of North Mill Pond and CuttsCove. Bridges and causeways acrossriver channels, bays and inlets as well assalt marshes have also probably led tothe destruction of many seagrass bedsand marshes along the seacoast. Shore-line development for marine related usescontinues to impact marshes eelgrassbeds today. For example, potentialimpacts from the Port of New Hampshireexpansion are outlined in the mitigationplan (Short et al., 1992), which identifiesspecific eelgrass beds, mud flats and saltmarshes as three estuarine habitats thatmay be impacted from port expansion(see habitat mitigation section below).

Anthropogenic inputs of contami-nants to the estuary resulting from devel-

Year Shoot Rhizome Eelgrass Biomass Algal Morphology WastingDensity Length Shoots R&R Total Biomass Length Width Leaves Disease Index

#/m2 cm/m2 grams dry wt./m2 g/m2 cm mm #/shoot %

1987 427 197 66 263 114 5.0 4.7 16.61989 504 249 128 377 125 5.2 4.8 43.51993 426 139 395 59 454 25 145 4.9 3.8 10.0

Population characteristics of eelgrass in the small beds at the mouth of Great Bay (near the rednun buoy): August 1987, 1989, 1993.

TABLE 3.8

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FIGURE 3.19

Eelgrass distribution in Great Bay and Little Bay: 1981.

opment within the watershed may havesignificant indirect impacts on eelgrasshabitat. Potential impacts were outlinedfor Great Bay Estuary (Short, 1992), andhave been documented in other NewEngland estuaries (Short et al., 1995;Short and Burdick, 1996). They includeeelgrass loss from nutrient over-enrich-ment and increased sediment input. Theprimary cause of these eelgrass losses isreduction in water clarity, a result ofhuman impacts to the estuarine water-shed. Anthropogenic impacts to eelgrasshabitat within the Great Bay Estuary havenot been documented.

Seagrass has been harvested in thenortheast for building insulation, uphol-stery stuffing, but is probably most wide-ly used for garden mulch and fertilizer.The scale of such activities in New

Hampshire do not appear to have beenlarge, and although their potentialimpacts are unknown, they are likelyminor.

3.3.3.3 Habitat Change Analysis and Modeling

The spatial distribution of eelgrass habitatin Great Bay has been modeled using aspatial grid modeling structure (Short etal., 1996). The model calculates and pre-dicts the changes in eelgrass habitat thatresult from poor water quality and wast-ing disease activity (Short et al., 1986;1995) after incorporating tidal flows withdistributions of water quality characteris-tics available from throughout the GreatBay Estuary (Jones and Langan, 1994a).Eelgrass habitat modeling in the GreatBay Estuary is now limited by the lack of

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adequate hydrodynamic information tofully implement the spatial distributionmodel. With such information, the modelwill continue to improve and become auseful predictor of eelgrass habitat distri-bution. This management tool can thenbe expanded to incorporate other estuar-ine habitats, including salt marsh, algalbeds, and shellfish areas.

Change analysis of eelgrass distribu-tion in the Great Bay Estuary has provid-ed valuable information for understandingthe dynamics of the eelgrass habitat. Aloss of eelgrass distribution in Great Baywas documented between 1981 and 1984for Great Bay, Little Bay and the upperPiscataqua River (Short et al., 1986). Thedramatic losses of eelgrass over this timeperiod signalled a recurrence of the wast-ing disease. This disease devastated eel-

grass populations in the 1930s along bothcoasts of the North Atlantic (Short et al.,1988). The wasting disease was subse-quently shown to result from a pathogen-ic infection of eelgrass populations by amarine slime mold Labryrinthula zosterae(Short et al., 1987; Muehlstein et al., 1991).

More recent change analysis in GreatBay has documented further loss of eel-grass through the remainder of the 1980s(Figure 3.18) to a low point in eelgrassdistribution in July, 1989. This dramaticdecline in eelgrass was followed by anequally dramatic increase and recoveryof eelgrass beds that occurred between1989 and 1990 (Burdick et al. 1993). Theloss during the 1980s was determined tobe caused by rapid infection and spreadof Labryrinthula zosterae. The spread ofthe disease ceased in late 1988 following

FIGURE 3.20

Eelgrass distribution and density in Great Bay

and Little Bay: 1990.

a rainfall event which decreased thesalinity of the estuary and inhibited thegrowth of the pathogen. The recovery ofeelgrass during 1989 through 1990 wasthe result of high levels of sexual repro-duction and seed dispersal within theestuary producing extensive revegetationof mudflat areas by eelgrass seedlings.

The total area of eelgrass loss inGreat Bay between 1986 and 1989 was690 hectares (ha) and the area of recov-ery from 1989 to 1990 was 700 ha. Thischange analysis suggests that the loss ofarea was extremely rapid at 230 ha/ybut that the recovery through seedlingrecruitment was even greater, over 600ha/y. The rapid recovery due to recruit-ment of new shoots from seeds hadactually begun in 1989, but did notshow until the 1990 aerial photographs.The 1992 maps indicate more extensiveeelgrass cover in Great Bay than wasreported by Nelson (1981) (Figures 3.19and 3.20).

As of 1990, distribution of eelgrass inLittle Bay was approximately 2% (Figure3.20) of what was reported in Little Bayin 1981 (Figure 3.19; Nelson 1981), how-ever the source of the data and the meth-ods used by Nelson (1981) are unclear.The most recent published map of eel-grass in Little Bay (Burdick et al. 1993)includes a persistent bed off Dover Pointand a small bed just west of the GeneralSullivan Bridge in Newington. A decadeprior to these observations, Nelson(1981) reported eelgrass along both sidesof Little Bay and extending into the Bel-lamy River. Little Bay has been moni-tored annually from 1984 to the present,and no new patches of eelgrass werefound prior to 1993. Since 1993, naturalrecruitment of new eelgrass beds hasoccurred at 3 sites in Little Bay. The lossin area of eelgrass in Little Bay from 218ha in 1981 (Nelson 1981) to 3.7 ha in1990 (Burdick et al. 1993) shows a loss of98% of the eelgrass in Little Bay over that9 year period. The increase from 1993 tothe present has not been quantified. In1997, an effort was begun to restore eel-grass to parts of Little Bay (see section onHabitat Restoration).

In the Piscataqua River, eelgrass iscurrently found in small beds along theshoreline in many areas. On the Maineside of the Piscataqua River, the mostextensive bed of eelgrass exists offAddlington Creek just south of the con-fluence of Little Bay and the upper Pis-cataqua River. Small patches of eelgrassare found further down the PiscataquaRiver on the Maine side and adjacent tothe small boat passage under the Memo-rial Bridge. On the New Hampshire sideof the river, eelgrass is found in OuterCutts Cove adjacent to the New Hamp-shire Port Authority construction and atseveral sites along the Piscataqua southof Dover Point where eelgrass restora-tion has taken place as part of the NewHampshire eelgrass mitigation project(Short et al., 1996; Davis and Short,1997).

Using the 1981 NH Fish and Gamemap of eelgrass distribution in the Pis-cataqua River as a baseline, (Nelson,1981) data from 1990 (Burdick et al.,1993) indicate that there was a loss ofapproximately 50 ha of eelgrass in a tenyear period. The restoration of 3.5 acresof eelgrass habitat along the NewHampshire side of the Piscataqua River(Short et al., 1996) has increased thearea of eelgrass in the river, howeverchanges in the existing eelgrass areasfrom 1990 to 1997 have not been docu-mented. In Portsmouth Harbor, eelgrasshas not been carefully mapped and nohistorical data has been reported, butobservations of eelgrass beds over thepast decade suggest fairly consistent dis-tribution (Short, 1992; Johnston et al.,1994) . Eelgrass has been foundthroughout many parts of PortsmouthHarbor with extensive beds at themouth of the Harbor on both the NewHampshire and Maine side. At thesesites, eelgrass grows to a maximumdepth of 11 meters as a result of clearwater from the Gulf of Maine enteringthe River. More comprehensive map-ping of eelgrass distribution in the entireGreat Bay Estuary is needed to establishbaseline conditions for future habitatmonitoring and change analyses.

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3.4

WILDLIFE Because of the diversity of habitats,

New Hampshire’s estuaries supportan impressive array of living resources.In addition to the species describedabove, terrestrial wildlife, birds andmarine mammals are also present. Mam-mals living within the Great Bay areainclude whitetail deer, beaver, red fox,mink, otter, muskrat, coyote and rac-coon. In addition, Great Bay is part ofthe Atlantic flyway and an importantmigratory stopover as well as winteringarea for many birds. As a result, there aresubstantial populations of both seasonaland year round birds that undoubtedlyhave a direct affect on water qualitythroughout the coastal zone.

3.4.1 MARINE MAMMALS

Harbor seals (Phoca vitulina) may befound throughout the Great Bay Estuary,and are common in the lower portions ofthe estuary as well as in Rye Harbor andHampton Harbor. A hooded seal wasseen in Little Bay in 1998. Harbor por-poises (Phocoena phocoena) frequentthe lower portions of the estuary andhave been sighted in Little Bay. It is like-ly that some whales find their way intoPortsmouth Harbor (e.g., a humpbackwhale, Megaptera novaeangliae sp. trav-elled up the Piscatatqua River to themouth of Little Bay in 1995). There arealso maps for sightings of 5 whalespecies in the Gulf of Maine that includesightings off the coast of New Hampshire(CeTAP, 1982 in NAI, 1994). Harbor seals(Phoca vitalina) were the only marinemammal observed in a study whereweekly observations were made for 12months during 1980-81 throughout theGBE (Nelson, 1982). Seals were sightedfrom November through April, mostoften during March and April. They weresighted most often in Little Bay, withinfrequent sightings in Great Bay and thePiscataqua River. Data maintained byNOAA/NMFS indicates an increase inharbor seal populations throughout theNew England region, confirming obser-vations by local fishermen as well as

impingement data from the SeabrookStation Environmental Studies (NAI,1996).

3.4.2 WATERFOWL AND SHOREBIRDS

The Seacoast area is the principal winter-ing waterfowl location in New Hamp-shire (Vogel, 1995), with 75% of thewintering waterfowl in Great Bay. Arecent mid-winter survey of mallards,black duck, greater/lesser scaup, golden-eye, bufflehead, red-breasted mer-gansers, Canada geese and otherseaduck species showed Canada geeseand black duck to be the most plentifulspecies around Great Bay (Vogel, 1995).The 1995 counts for most species werehigher than the average count for theprevious ten years. Recent counts forwaterfowl by the Audubon Society in theHampton Harbor area are presented inTable 3.9.

Great Bay is a focus area for theNorth American Waterfowl ManagementPlan (Vogel, 1995). There are twowildlife preserves in the Great Bay area.One is located in Newington at the siteof the old Pease Air Force Base. It con-sists of a 1,054 acre area bordering LittleBay which has been designated as aWildlife Sanctuary by the U.S. Fish andWildlife Service. The other preserve islocated at Adams Point and is adminis-tered by the NH Fish and Game Depart-ment as a Wildlife Management Area. Inaddition, the Great Bay EstuarineResearch Reserve has over 5,300 acres ofprotected areas that include wetlands,

Piping plover chick

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saltmarshes, uplands and habitat forwaterfowl. Other conservation areasinclude Audubon’s Bellamy River prop-erty, Nature Conservancy land onDurham Point and other NH Fish andGame areas.

A detailed study of shorebird use ofthe Great Bay Estuary during the fall andspring migratory periods was conductedin 1990-91 (Miller and Miller, 1991). Dataon the relative abundance of 16 shore-bird species during a one year periodwere reported along with habitats used,locations, human influences, manage-ment options and research needs. Thereis a checklist for the birds of Great Baythat lists >170 species by season andabundance (GBNERR, 1993).

3.4.3 NON-GAME SPECIES

A summary of the amphibians, reptiles,mammals and wetland-associated birdsin New Hampshire is included as a seriesof appendices in Chase et al. (1995). Theappendices cover terrestrial and semi-ter-restrial vertebrates with a few exampledescriptions of habitat use, survivalneeds and conservation issues. In NewHampshire there are 39 species ofamphibians and reptiles, 55 native mam-malian species and over 200 bird species,51 of which they list as wetland-depend-ent or wetland-associated. Bald eagles,common terns, upland sand pipers,marsh hawks, ospreys and common

loons are endangered and threatenedbird species found in the Great Bay Estu-ary (Merrill, 1995). The bald eagle inhab-its the shores of Little and Great Bay inthe winter (NH Audubon Society, annualmonitoring data).

A study consisting of weekly birdobservations made for 12 months during1980-81 throughout the GBE identifiedover 90,000 consisting of 71 species (Nel-son, 1982). The birds were classified intofour categories: seabirds, waterfowl,wading birds and terrestrial and shore-birds. Some species left the area duringcold months and were replaced to someextent by other species. The total speciesin the estuary each month was fairly con-stant at ~20, ranging from 13 in Januaryto 34 in August.

Great Bay is part of the Atlantic fly-way and an important migratorystopover as well as wintering area formany waterfowl and wading birds. As aresult, there are both substantial season-al and year round populations of water-fowl throughout the Great Bay area.Common species include cormorants,Canada geese, bald eagles, sea gulls,terns, ducks, herons, snowy egrets,common loons and a large variety ofperching birds.

Wildlife is well represented withinthe Little Harbor area, primarily at Odi-orne State Park, and in the extensive saltmarshes of Seavey Creek and Berry

Species 1995 Counts 10 Year Average Change from 1995 Volunteer(1985-1994) 10 Year Averages Count Averages

Mallard Anas platyrhynchos 511 288 77% 493Black duck Anas rubripes 1,846 973 90% 267Greater/lesser scaup Aythya marila/affinis 550 360 53% 114Goldeneye Bucephala clangula 200 79 153% 50Bufflehead Bucephala albeola 0 5 — 43Seaduck species 513 436 18% 0R.B. merganser Mergus serrator 7 8 –13% 26Canada goose Branta canadensis 3,110 1,603 94% 1,821

Total 6,796 4,200 62% —

Volunteer data based on the average counts of 6 surveys conducted January-March, 1995 at certain sites around Great Bay. Other speciesnoted during the volunteer survey include domestic geese, mute swans, hooded mergansers, common mergansers, northern pintails,ruddy ducks, and ring-necked ducks.

Summary of mid-winter survey and volunteer counts of waterfowl in Hampton Harbor: 1995.Data from Vogel (1995).

TABLE 3.9

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Brook, part of which is owned and man-aged by Odiorne State Park. Habitatareas in Little Harbor have been mapped.Mammals living in the Little Harbor areainclude whitetail deer, beaver, fox, mink,otter, muskrat, squirrels, chipmunks, rab-bits, moles, voles, rats, mice, bats,shrews, weasels, skunks and raccoons(Seacoast Science Center, 1992). Wildlifepopulations are not suspected to be largeenough to impact water quality, espe-cially considering that most of the shore-line is developed. In addition, the LittleHarbor area is a seasonal stopover formany waterfowl and wading birds.Species seen or heard during one ormore seasons include common loon,grebes, cormorants, bittern, brant, Cana-da geese, mallard, eider, oldsquaw, scot-ers, common goldeneye, bufflehead,mergansers, hawks, kestrel, plovers,killdeer, yellowlegs, willet, sandpipers,godwits, turnstone, dunlin, snipe, gulls,terns, dovekie, owls, whip-poor-will,swift, kingfisher, woodpeckers, flicker,flycatchers, phoebe, kingbird, swallows,jays, crows, chickadee, nuthatches,wrens, kinglets, wheatear thrushes,robin, catbird, mockingbird, cedarwaxwing, starling, vireos, warblers, paru-la, warblers, redstart, yellowthroat, pineand evening grosbeak, towhee, sparrowsblackbird, grackle, orioles, finches, cross-bill, goldfinch, and a large variety of lesscommon birds.

3.4.4 RARE ANDENDANGERED SPECIES

There are a number of threatened andendangered species in coastal NewHampshire. There are 23 threatened orendangered plant and animal species inthe GBNERR. The shortnose sturgeon isa federal endangered species that proba-bly occurs, although this is unproven(NAI, 1994). Detailed descriptions of thesix endangered and threatened birds inthe coastal region were given in NHOSP(1992). The bald eagle is federally listedas endangered and it occurs in theSalmon Falls, upper Piscataqua, Oyster,Cocheco and Bellamy rivers plus in LittleBay, Great Bay and tributaries,Portsmouth Harbor and Back Channel

area, and in Hampton Harbor and itstributaries. It also probably occurs in theExeter and Lamprey rivers plus Rye Har-bor. The piping plover is federally listedas threatened and occurs in parts ofHampton Harbor and its tributaries. Theperegrine falcon, once federally listed asendangered but now delisted, has docu-mented occurrences in the upper Pis-cataqua River and in Hampton Harborand its tributaries. A more comprehen-sive list of threatened or endangeredspecies in the GBNERR is in Appendix L.

Foss and De Luca (1992) assessedthe breeding season distribution, habitatuse, status and nesting success of fourthreatened or endangered bird species incoastal New Hampshire. The speciesincluded common terns (state endan-gered), ospreys (state threatened),norther harriers (state threatened) andpiping plovers (state endangered; feder-ally threatened). Tern colonies werelocated in Hampton marsh, Back Chan-nel and Little Bay. Northern harriers usedcoastal habitats in 1992, but there was noproof of nesting. Piping plover habitatexists on the southeast shore of Hamp-ton Harbor, but no breeding wasobserved in 1992. Osprey nests in fourlocations were monitored and somebreeding activity was observed. Thereport included monitoring and manage-ment recommendations for each species.Others have continued monitoring thefour existing osprey nests around GreatBay (C. Martin, NH Audubon Society,personal communication).

In 1997, the NHOSP funded a proj-ect by the NH Audubon Society and theNHF&G Department Nongame Programto restore terns to the Isles of Shoals(NHF&G, 1997a). Seven chicks hatchedfrom six nests, and efforts will be madeto repeat this success next year. TheNHF&G Nongame Program also protect-ed and monitored five piping plovernests at Seabrook and Hampton beachesin 1997. Three of the seventeen chickssurvived and fledged in August. The oth-ers either starved or were run over byvehicles or joggers. This was the firstdocumentation of nesting piping ploversin New Hampshire since 1984.

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The objective of this section is to syn-thesize current information on select-

ed species relevant to shellfish and otherliving resources, not necessarily to be acomprehensive review of all introducedand nuisance species.

3.5.1 GREEN CRABS (Carcinus maenas)

Introduced and Nuisance Green crabs were introduced into NorthAmerica in the early 1900’s and havebeen identified as a major predator ofjuvenile shellfish. In the Great Bay Estu-ary, green crabs are more abundant inthe Piscataqua River and Little Bay thanin Great Bay. Though there is someinformation on crab density at eelgrassmitigation sites in the Piscataqua River,the data are insufficient to establish thestatus and trends of green crab popula-tions in Great Bay. Normandeau Associ-ates Inc. has monitored green crabpopulations in Hampton Harbor since1977 using baited traps (NAI, 1996).Their data show that crab density in agiven year is highly dependent on theminimum winter temperature, and thatcolder temperatures result in fewer crabsthe following spring (Savage and Dun-lop, 1983). Survival of clam spat appears

to be negatively correlated with crabdensity (NAI, 1996). Green crabs as wellas rock crabs (Cancer irroratus) andmud crabs (all of which are abundant inGreat Bay) also prey on juvenile oysters.Green crabs have been identified as seri-ous pests that threaten efforts to restoreeelgrass beds in the Great Bay Estuary.Descriptive study and mesocosm experi-ments have shown that their foragingand burrowing activities kill and dislodgeplanted shoots (Davis et al., in review).

3.5.2 EUROPEAN OYSTER (Ostrea edulis)

IntroducedDiscussed in another section.

3.5.3 COMMON PERIWINKLE (Littorina littorea)

IntroducedThis introduced species is highly abun-dant in coastal and estuarine waters. As agrazer, it is primarily herbivorous, butwill scavenge on detritus as well.Through its foraging activities, the com-mon periwinkle has a significant role inestuarine food webs, and influences (andmay control) community patterns alongrocky shorelines (Mathieson et al., 1991).However, the widespread distribution ofthis 19th century colonizer has left ecol-ogists with little opportunity to collectevidence and test whether Littorina lit-torea has caused adverse impacts oncoastal and estuarine ecosystems in theGulf of Maine.

3.5.4 OYSTER DRILL (Urosalpinx cinerea)

Nuisance The oyster drill, a predatory gastropod,preys heavily on oysters in higher salini-ty waters. Intolerant of low salinities,drills typically cannot survive extendedperiods in areas of Great Bay wheremajor oyster beds are located, althoughthey have been found at Nannie Islandand Adams Point. During extended highsalinity periods, they can cause signifi-cant mortalities. The status and trends of

3.5

INTRODUCED AND NUISANCE SPECIES

Green crab

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drill populations, and their impact onoyster population has not been docu-mented.

3.5.5 SEA LETTUCE (Ulva lactuca)

NuisanceProliferation of ephemeral green algaesuch as Ulva latuca due to nutrientoverenrichment has caused seriousecosystem alterations in many areas ofthe world (Sawyer, 1965). Though severeimpacts have not been documented inthe Great Bay Estuary, anecdotal obser-vations of increased abundance of Ulvalatuca and other opportunistic greenalgae should prompt some analysis ofthe change in areal coverage and bio-mass of these so called “nuisance”macrophytic algae. A project thataddresses this subject began in 1997 andis described in section 2.4.5.3.

3.5.6 OTHER INTRODUCED AND NUISANCE PLANTS

The major nuisance species associatedwith declines in seagrass habitats world-wide are various species of algae, includ-ing opportunistic red and green speciesthat form mats and drift into beds, epi-phytic species that cover individualblades, and phytoplankton that canshade entire beds (Short and Wylie-Echeverria, 1996). Although epiphytesand drift algae are known to occur inseagrass beds in New Hampshire’s estu-aries, impacts to eelgrass beds do notappear to be significant at this time(Short et al., 1993; Langan and Jones,1993). However, experimental modelecosystems of eelgrass beds indicate thatnutrient additions can lead to algal dom-inance and seagrass bed collapse (Shortet al., 1995).

In New Hampshire, Widgeon grass(Ruppia maritima) occurs primarily increeks, ponds, and pannes of salt marsh-es (Richardson, 1980). However, it alsooccurs extensively in South Mill Pond,Portsmouth, where it must compete withvarious species of opportunistic macroal-gae. What little is known about habitatchange regarding the macroalgal beds of

New Hampshire estuaries includes stud-ies on the destruction of estuarine andnear shore populations of kelp by asmall species of estuarine snail, Lacunavincta (Fralick et al., 1974) and previous-ly mentioned increases in macroalgalhabitat by Ulva latuca and other oppor-tunistic species.

Several species of emergent plantsare considered nuisances in tidal marsh-es. These include common reed (Phrag-mites australis, formerly communis),purple loosestrife (Lythrum salicaria),and sometimes cattail (Typha angustifo-lia) (USDA, 1994).These plants drasti-cally reduce plant diversity in marshes,restrict bird and fish access to themarsh, and have been cited as a firehazard to nearby homes (USDA, 1994;Rozsa, 1995). The presence and spreadof these species can serve not only asindicators of impacts to marshes (USDA,1994), but as indicators of losses inmarsh functions and values (Morgan etal., 1996). Thus, these invasive plantsare believed to reduce the economicvalue of salt marshes (USDA 1994). Allthree species are clearly increasing incoastal marshes (Dzierzeski, 1991;USDA, 1994; Tiner, 1996). Phragmites iscited as the “most significant problemconfronting” salt marshes in Connecticut(Rozsa, 1995), and its continued spreadand establishment in New Hampshiremarshes is cause for concern. Manage-ment action plans have been developedand implemented to curb this problem.For example, where these plants haveinvaded tidally-restricted marshes,reestablishment of natural tidal regimeshave reduced their distribution or vigor(Burdick and Dionne, 1994; Burdick etal., 1997).

Within salt marshes, human nui-sances such as mosquitos and green-head flies are managed by seacoasttowns that collectively spend approxi-mately $100,000 each year. Ironically,most of the effort to control these pestsoccur in marshes that have degraded,often as a result of efforts to managesuch pests (USDA 1994).

The review of technical information on the status and trends for living resources incoastal New Hampshire showed a great deal of existing information for a wide rangeof different species and communities. There are issues that emerge from analysis of thedata for some species, while little is known about others. This section is a summary ofwhat is known and what information gaps still exist.

� The species richness and dominant species found in communities of benthicinvertebrates in the Great Bay Estuary were essentially unchanged from1972 to 1995.

� A few benthic invertebrate and macroalgae species are disjunct warm-watertaxa, with their northernmost contiguous distribution limit occurring south ofNew Hampshire.

� Eastern oysters are found mainly in the Great Bay Estuary in coastal NewHampshire.

� Eastern oyster populations in the Great Bay Estuary have undergone amarked decline during the past half century.

� The first recorded MSX epizootic in the Great Bay Estuary occurred in 1995.There was a high rate of mortality in the upper Piscataqua River and tidalSalmon Falls River, and a lower rate of systemic infections in the rest of theEstuary.

� The causative agent of Dermo disease in oysters, Perkinsus marinus,wasidentified in oysters from Spinney Creek in September, 1996. A low preva-lence of Dermo infections have also been found in oysters from Great Bayand the Oyster River.

� European flat oysters, razor clams, ribbed mussels, the gem clam and rock,green, mud and horseshoe crabs are found in numerous areas of coastalNew Hampshire.

� Softshell clams are found in high densities in Hampton Harbor and in mod-erate to high density in flats in the Salmon Falls River and near Sandy Pointin Great Bay. Clams are present at low densities in Little Bay, Great Bay andLittle Harbor.

� In the Great Bay Estuary and Little Harbor, clam populations are a fractionof their historical levels.

� In Hampton Harbor, clam populations were abundant in the mid-1970s and1980s, with a sharp decline starting in 1984, likely due to heavy harvestpressure. The decline was also a result of sarcomatous neoplasia, a form ofleukemia in clams.

� Blue mussels are found in all New Hampshire’s estuaries and open coast,except in the upper reaches of tributaries where low salinity limits their sur-vival. Their abundance has not been documented, and their density can beas high as 3500/m2 in Hampton Harbor.

� Sea scallops can be found in Portsmouth Harbor with an average density of1.3 scallops/m2 and an even distribution of sizes.

� Lobster populations are relatively stable throughout coastal New Hampshire, despite increasing fishing pressure.

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3.6

SUMMARY OF FINDINGS

167

� A tremendous increase in the seasonal occurrence of striped bass hasoccurred in New Hampshire in the past decade, probably as a result of an earlier region-wide moratorium and other harvest restrictions.

� The recreational catch per unit effort of winter flounder has declined inGreat Bay over the last decade, probably as a result of heavy commercialfishing in the Gulf of Maine.

� The abundance of rainbow smelt and river herring has been highly variableover the last decade.

� New Hampshire has approximately 50% of its 18th century tidal wetlands,or about 7,500 acres. Plants found in these areas include cord, spike andblack grasses.

� Marine and terrestrial development pose the greatest current threat to saltmarshes.

� Tidal restrictions are relatively widespread, affecting 21% of the salt marsharea in New Hampshire.

� There are 219 known species of seaweeds found along the rocky shorelinesand the subtidal photic zones of areas throughout coastal New Hampshire.Dredging and development pose threats to macroalgal habitats.

� Eelgrass habitat is a significant component of the Great Bay Estuary ecosys-tem. Distribution maps, some over time, have been compiled for manyareas of coastal New Hampshire.

� Eelgrass populations experience dramatic temporal and spatial changes. A dramatic decline occurred in the late 1980s in Great Bay at a rate of 230ha/y, followed by a rapid recovery after 1989, at a rate of 600 ha/y. Thedecline was a result of a wasting disease.

� Harbor seals, harbor porpoises are commonly found, especially in lowerGreat Bay Estuary, Rye Harbor and Hampton Harbor. An occasional othermarine mammal such as humpback whales has also been seen.

� The Seacoast area is the principal wintering location for waterfowl in NewHampshire, 75% of which are in Great Bay. Counts of most species made inHampton Harbor during 1995 were higher than the average from the previ-ous ten years.

� There are 23 threatened or endangered animal and plant species in theGreat Bay National Estuarine Reserve. Monitoring and habitat restorationprojects are being conducted for bald eagles, ospreys, common terns andpiping plovers.

� Introduced and nuisance species of particular concern in coastal NewHampshire include green crabs, European oysters, common periwinkle, oys-ter drill, sea lettuce, common reed, purple loosestrife, mosquitos and green-head flies.

169

he Great Bay and Hampton/Seabrook estuaries are extremelyimportant to the local, regional,

state, and national economies. From thetime of first European settlement, theGreat Bay Estuary has been a center ofcommerce for natural resource basedindustries such as commercial fishingand logging. During the 19th century,shoe and textile manufacturing becameimportant and mills were built in alltowns with access to navigable water-ways. Today energy is produced in facil-ities located on the Piscataqua River andin Hampton Harbor, and the shipping oflumber, mineral salt, gypsum and otherproducts is of significant economicimportance. Several species of fish stillsupport local and regional fisheries in theGulf of Maine, and tourism and recre-ation are becoming increasingly impor-tant parts of the N.H. Seacoast economy.Many of these activities are dependenton good water quality and a healthyecosystem. In particular, habitat degrada-tion and declines in important fish andshellfish species remain a concern. Thischapter summarizes what is knownabout human uses and resource man-agement in Coastal New Hampshire toframe related issues and to assess the sig-nificance of problems and informationgaps relative to the Seacoast’s estuarineecosystems.

4 HUMAN USES AND RESOURCE MANAGEMENT

T

Oytersmen

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4.1

POPULATION TRENDS, EMPLOYMENT AND INCOME

4.1.1 POPULATION AND DENSITY TRENDS AND PROJECTIONS

The human population trends forRockingham and Strafford counties

from 1970 to 2015 (NHOSP, 1997a) areshown in Figure 4.1. Both Rockinghamand Strafford counties had more dra-matic increases in population from1970-1990 compared to projectedincreases from 1990 to 2010. Rocking-ham County increased from 138,951 to245,845 people from 1970 to 1990, a77% increase while the increase was36% in Strafford County. The popula-tions are projected to increase from1990 to 2010 by 48% in RockinghamCounty and by 18% in Strafford County.Throughout the 40 year span of data,the population of Rockingham County

has been and is projected to continue tobe greater than Strafford County.

Figure 4.1 shows population densi-ty trends and projected trends through2015. The population density of Straf-ford County has been greater than forRockingham County, with the differenceprojected to narrow as densities in bothcounties continue to increase through2015. In 1990, 50.4% of the people inRockingham County were female and51.6% of the people in Strafford Countywere female (NHOSP, 1997a). The con-tinuation of increases in population anddensity in New Hampshire’s two coastalcounties is a concern because of theaccompanying increases in develop-ment, use of coastal resources and pro-duction of pollutants.

0

100

200

300

400

500

600

700

1970 1980 1990 1996 2000 2005 2010 2015

70,43185,408

104,233 109,135 113,409 119,451 122,431 128,048

99,029

367,621

190,345

245,845258,775

285,142

313,077

335,203

DensityOffice of State Planning Projections

Strafford Density

Rockingham Density

Strafford Population

Rockingham Population

Density in People per Square Mile

FIGURE 4.1 Population growth in Rockingham and Strafford counties, New Hampshire: 1970-2015.

171

4.1.2 EMPLOYMENT AND INCOME

The economic issues in coastal NewHampshire have been reviewed innumerous studies (Colgan, 1995; NAI,1994; Ogrodowczyk, 1993). Much of thework focused on fisheries, but tourism,transportation, industries, and relatedissues were also discussed. Table 4.1,shows the harbor-related economic valueand jobs generated by coastal industries(NAI, 1994). Table 4.2 shows wherethese activities occur in New Hampshire.The different activities take placethroughout the Seacoast, but PortsmouthHarbor is the only place where all activ-ities occur, while recreational boating isthe only activity that occurs at all sites.Little Harbor anticipates an increase inrecreational boating and PortsmouthHarbor anticipates an increase in com-

mercial shipping; the rest of the harborsanticipate maintenance of similar levelsof activities, which have been mostlyrecreational (NAI, 1994). Maintenance ofcurrent activities will require mainte-nance dredging, and reduced dredgingwould seriously impact cargo shipping,shipbuilding, cruise ship operations, andcommercial fishing.

As shown in Table 4.1, commercialfishing is the industry type with the largestemployment and economic activity. Itencompasses the fishing, hunting, trap-ping, fresh or frozen prepared fish, andwholesale trade categories of economicactivity. Rockingham County has the vastmajority of jobs and economic activity.More information on the present status ofthe commercial fishing industry is provid-ed below in the Commercial Fisheries andAquaculture section (4.3.1.3).

Industry Value in $ Jobs

commercial fishing 160 million 1065recreational boating 18 million 55cargo shipping 12 million 91boatbuilding and repair 2.1 million 56water transportation/tourism 1.7 million 14

Total 193 million 1281

The economic value and jobs generated by coastal New Hampshire industries. TABLE 4.1

Cargo Commercial Boat Recreationalterminal Tourism fishing yards Ferry boating Other

RiverSquamscott R. — — x — — xLamprey R. — — x — — xOyster R. — — — — — xCocheco R. — x x x — x

Harbor/BayGreat Bay — — — — — xLittle Bay — — x x — xPortsmouth Harbor x x x x x x (tugs, barges)

Portsmouth back channels — — x — — xLittle Harbor — x x — — xHampton Harbor — x x x — xIsles of Shoals — x x — x x

Harbor-related activities in New Hampshire.TABLE 4.2

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4.2

LAND USE AND DEVELOPMENT ISSUES

Residential Ttl area Remaining Remaining Ttl developed Ratio ofPopulation Total area area developed undevelopable developable area per remaining to ttl

Town 1992 (acres) (acres) (acres) (acres) (acres) capita developable land

Dover 25114 18587 4318 6363 2826 9398 0.25 0.60Durham 12348 15852 1865 2561 3181 10110 0.21 0.80Exeter 12356 12813 2646 3452 1982 7379 0.28 0.68Greenland 2790 8524 1259 1879 2719 3926 0.67 0.68Hampton 12269 8901 2391 3319 2794 2788 0.27 0.46Hampton Falls 1531 8078 948 1430 1797 4851 0.93 0.77Madbury 1431 7799 649 954 1629 5217 0.67 0.85New Castle 831 1218 301 372 773 73 0.45 0.16Newfields 909 4647 340 491 703 3453 0.54 0.88Newington 688 7916 578 3757 2784 1375 5.46 0.27Newmarket 1796 9080 1715 2056 2195 4829 1.14 0.70North Hampton 3642 8914 1913 2414 1637 4863 0.66 0.67Portsmouth 22342 10762 2459 6123 2513 2127 0.27 0.26Rochester 26640 29072 5252 8007 2504 18561 0.30 0.70Rollinsford 2646 4840 178 896 619 3325 0.34 0.79Rye 4555 8353 2205 2716 2375 3262 0.60 0.55Seabrook 6537 5923 1407 2239 1920 1764 0.34 0.44Sommersworth 11239 6396 1574 2351 801 3244 0.21 0.58Stratham 5040 9902 2619 3226 1396 5280 0.64 0.62

Total 154704 187578 35155 54607 37146 95825 0.35 0.64

Notes: “Developed” land data from regional planning commission land use maps, circa 1992.“Remaining Undevelopable” land includes protected land, surface water, large wetlands, road and transmission rights of way, and other land types unsuitable for development.

Developed and undeveloped acreages in the 19 coastal New Hampshire municipalities.TABLE 4.3

4.2.1 URBAN AND RURAL DEVELOPMENT

The assessment of water quality and liv-ing resources in coastal New Hampshirebenefits from addressing issues at largescales. An assessment of the land useand human activities that occur on theuplands and in the watersheds adjacentto New Hampshire’s estuaries helps inthe understanding of processes thataffect human health issues and theintegrity of the estuarine ecosystems.

Published land-use change informa-tion is limited (Coppelman et al., 1978;Befort et al., 1987; NHCRP, 1997). Datafrom the Complex Systems ResearchCenter at UNH are also available. Agri-cultural land in New Hampshire hasdecreased in Rockingham and Straffordcounties from 472,000 acres in 1850 to

42,000 acres in 1996, while urban landscomprised 13.9 and 8.5% of Rockinghamand Strafford counties, respectively, in1996 (NHCRP, 1997).

A critical lands analysis project con-ducted for the NHEP by the ComplexSystems Research Center at UNH is deter-mined the potential for development inuplands classified by land use (Rubinand Merriam, 1998). The quantity andquality of the existing information variedfor each town or city in the coast. Inaddition, policy and program reviews oflocal, state and federal regulations gov-erning land use and human activities inthe region have also been conducted(Carlson et al., 2000; 1997).

Some of the results of the criticallands analysis are summarized in Table4.3. Data for all of the 19 coastal NewHampshire municipalities include popu-

173

lation, total acres, residential area, totaldeveloped area, and the remaining landthat is either undevelopable or devel-opable. For comparisons of differentsized municipalities, a ratio of total devel-oped area per capita is provided. New-ington has the highest ratio (5.46) by far,reflecting both extensive developmentand a low population. Hampton Falls hasthe next highest (0.93) ratio, while Dover,Durham, Exeter, Hampton, Newmarket,Portsmouth, Rochester and Somersworthhave low (< 0.3) ratios. The eight munic-ipalities with the low ratios are also theeight with the highest populations.

Another way of comparing differentmunicipalities is to calculate the fractionof remaining developable land comparedthe total area of developed and devel-opable land (Table 4.3). A low ratio sug-gests that the municipality has less roomto continue development. The communi-ties with low (< 0.3) ratios are New Cas-tle, Newington and Portsmouth.Communities with high (> 0.7) fractionsare Durham, Hampton Falls, Madburyand Rollinsford. These trends are alsoillustrated in Figure 4.2, which also fac-tors in undevelopable land. In the caseof New Castle, the limited room to devel-

op is a combination of having the small-est percentage of remaining developableland and the largest percentage of unde-velopable land, along with a modest per-centage of developed land. Portsmouthand Newington have the highest per-centage (> 40%) of developed land andrelatively small percentages of remainingdevelopable land. The four communitieswith the smallest percentage of devel-oped land also had the largest percent-ages of remaining developable land. Forthe whole Seacoast, 29% of the land hasbeen developed while 51% remainsdevelopable, with 20% undevelopable(Figure 4.3).

Dov

er

Dur

ham

Exet

er

Gre

enla

nd

Ham

pto

n

Ham

pto

n Fa

lls

Mad

bury

New

Cas

tle

New

field

s

New

ingt

on

New

mar

ket

Nor

th H

amp

ton

Port

smou

th

Roch

este

r

Rolli

nsfo

rd

Rye

Seab

rook

Som

mer

swor

th

Stra

tham

Remaining developable

Undevelopable

Developed

Percent land development and potential in the 19 coastal New Hampshire municipalities. FIGURE 4.2

Developed

Undevelopable

RemainingDevelopable

51%29%

20%

Percent land development and potential forcoastal New Hampshire.

FIGURE 4.3

4.2.2 ESTUARINE SHORELAND

Figure 4.4 shows the percentage land usetypes within 300 feet of tidal waters.Comparison of Figures 4.3 and 4.4 showsthat despite similar percentages of devel-oped and undevelopable lands, there is amuch lower percentage of estuarineshoreland that remains developable andmuch more that is undevelopable, inlarge part because of land that is perma-nently protected or extensively regulated

along the state’s shorelines. There is 51%of the land in all 19 coastal communitiesthat remains developable (Figure 4.3)compared to only 24% of the land with-in the 300 foot shoreline buffer zone(Figure 4.4). The 16% of shoreline bufferzone lands that are permanently protect-ed or extensively regulated constitutes40% of the land that would otherwise beconsidered developable.

4.2.3 HABITAT LOSS AND FRAGMENTATION

Forest fragmentation is the major causeof land habitat degradation in NewHampshire (NHCRP, 1997). It is highestin Rockingham County compared to allNew Hampshire counties. The averageforest patch size is also smallest (39.8 A).In terms of road density, Rockinghamand Strafford counties are second andthird highest in the state, with 5.6 and 4.7mi/1000 A, respectively. Not only doesroad density help to further fragmenthabitats, but roughly 10% of the totalannual kills for bear and deer statewidewere by roadkill. Cars killed an averageof 18 bears, 153 moose and 861 deer peryear from 1984-1995 (NHRCP, 1997).

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Currentlydeveloped

Permanentlyprotected

Otherundevelopable

Vacant/developable

24%

16%28%

32%

Land use types within a 300-foot shorelinebuffer in New Hampshire tidal waters.

FIGURE 4.4

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4.3.1 COMMERCIAL USES

4.3.1.1 Shipping and Commercial Vessel Traffic

Information on shipping is availablethrough the New Hampshire PortAuthority (NHPA). Monthly records ofvessel arrivals and departures are record-ed, along with type of vessel, home port,name, cargo, tonnage loaded and ton-nage unloaded. Based on the NHPA data,the total tonnage decreased from 1990 to1996, with a relatively consistent tonnagebeing shipped during all months (Figure4.5).

NAI (1994) summarized the totalshipping tonnage for New Hampshire bydifferent categories for 1980 and 1992.The total shipping tonnage increasedfrom 2.8 million tons in 1980 to 4.2 mil-

lion tons in 1992. The largest commoditywas oil, comprising approximately 2 mil-lion tons during both years. The increasefrom 1980 to 1992 was from increases ofshipping for dry and bulk tonnage. Dur-ing 1980, the dry and bulk commoditiesincluded salt, gasoline and scrap metal,with propane, asphalt and gypsum beingprominent in 1992. Data from these morerecent studies can be compared to earli-er data. Total shipping tonnage inPortsmouth Harbor was 505,000 tons in1949, increasing to 1.2 million tons in1958 (NHWPC, 1960). The major com-modity in 1958 was residential fuel oil(~400,000 tons), followed by gasoline,gas oil, wood manufacturing, coal andgypsum, all with greater than 100,000tons. The new NHPA docking and stor-age facilities should eventually allow an

4.3

ESTUARINE AND MARINE

USES AND ISSUES

JanFeb

MarApr

MayJun

JulAug

SeptOct

NovDec

Total Tonnage

19901992

19941996

4,39

9,93

0

3,82

2,25

8

3,66

7,80

2

3,73

8,41

3

3,70

2,66

3

3,73

0,04

4

4,00

0,42

4

Monthly and annual shipping tonnage recorded by the New Hampshire Port Authority: 1990-1996. FIGURE 4.5

increase in cargo handled at the NHPAfacility from 300,000 to 1 million tons(NAI, 1994).

The most widespread harbor-relatedactivity in New Hampshire is commercialfishing. There were 428 commercial fish-ing vessels in New Hampshire in 1992,264 at slips and 139 at moorings (Table4.4; NAI, 1994). The highest number ofcommercial vessels were in Portsmouth(200) and Hampton (100) harbors. Therewere also 80 sports fishing, eight whalewatching, eight windjammer/charter sailand 13 harbor tour cruise vessels in NewHampshire during 1992 (Table 4.5; NAI,1994).

4.3.1.2 Dredge and Disposal

All known dredging in New Hampshirecoastal waters since 1950 has been sum-marized by NAI (1994). Dredging in tidalwaters is restricted to November 15-March 15 (seasonal restrictions), anddoes not occur during periods of fishmigration or larval settlement of shellfish.NHF&G will allow exceptions to dredgeschedules outside of the target dateswhen necessary. Most dredging hasoccurred to maintain and expand thecommercial and recreational uses of NewHampshire’s harbors (NHOF, 1979). TheNAI (1994) report recommended

176

Total Commercial Commercial VesselsVessels at Slips at Moorings

RiverSquamscott R. 33 15 17Lamprey R. 10 5 5Oyster R. 3Cocheco R. 20 10

Harbor/bayGreat BayLittle Bay 20 16 4Portsmouth Harbor 200 173 27Portsmouth back channels 12 12Little Harbor 30 20 10Hampton Harbor 100 25 61

Total 428 264 136Rockingham county 385Strafford county 23Both counties 20

Private commercial vessels in coastal New Hampshire in 1992 (NAI, 1994).TABLE 4.4

Sport Whale Windjammer/ Harbor Tours/Fishing Watching Charter Sail Day Cruises

RiverSquamscott R.Lamprey R.Oyster R.Cocheco R.

Harbor/bayGreat Bay 2Little BayPortsmouth Harbor 10 3 2 5Portsmouth back channelsLittle Harbor 30 0 4 4Hampton Harbor 20 5 2 2Isles of Shoals

Total 80 8 8 13

Tourist-related vessels in New Hampshire in 1992 (NAI, 1994).TABLE 4.5

177

expanded dredging in Rye, Hamptonand Portsmouth harbors to enhance safe-ty of navigation, improve recreationaland commercial facilities and expandmooring spaces. It also provides a sum-mary of historical dredging and disposalactivities, regulatory programs, a valua-tion of harbor economic uses and a pro-jection of future disposal needs in Maineand New Hampshire. Most of the 2.9 mil-lion cubic yards of dredging material wasdredged in Rockingham County, withthis material being dredged from fivewater bodies during 66 dredging events(Table 4.6). There were also two eventsin Strafford County (Little and Greatbays), amounting to only ~16,000 cubicyards of material.

Dredge materials have been dis-posed of within intertidal, nearshore,open water, upland or unknown loca-tions (NAI, 1994). Much of the materialwas dumped at the Cape Arundel, MEopen water site. Some RockinghamCounty material was subject to chemicalanalysis (see Chapter 2). Most sampleshad low to moderate concentrations ofmetals, DDT and PCBs. A high PCB con-centration (>2.9 ppm) was found in onesample from Hampton Harbor, and ahigh concentration (>125 ppm) of vana-dium was found in two samples fromRye Harbor. On the Maine side ofPortsmouth Harbor, high concentrationsof copper (>342 ppm), lead (>285 ppm),mercury (>3.0 ppm) and zinc (>43.6ppm) were measured in numerous sam-ples from the Portsmouth Naval Ship-

yard. As in the past, much of the futuredredged material in Hampton and Littleharbors will be available for beach nour-ishment or nearshore disposal; other-wise, it will be hauled to offshoredisposal sites.

4.3.1.3 Commercial Fisheries and Aquaculture

Lobsters

The commercial lobster industry in NewHampshire coastal waters, whichincludes Great Bay and Hampton/Seabrook estuaries, consists of 300 lob-ster fishers harvesting approximately $5-6 million in ex-vessel value of lobstersannually. Despite heavy fishing pres-sure, the lobster catch has been stablefor a number of years. Commercial land-ings of lobsters solely from the GreatBay Estuary and Hampton Harbor werenot available, but lobsters are fishedcommercially in all but the upper tidalreaches of the estuaries. Including alllobsters caught by the New Hampshirefishing fleet, there have been 1.1 to 1.8million pounds of lobster landedbetween 1992 and 1997 (Table 4.7), val-ued at $4.6-6.7 million (Table 4.8),based on National Marine Fisheries Ser-vice (NMFS) data. Research programsconducted by UNH and Sea Samplingprograms and dive surveys conductedby the NH Fish and Game Departmentand Normandeau Associates provideinformation on lobster populations, lob-ster habitat, and seasonal movements of

Number of AggregateHarbor Events (cy) Volume

Rockingham County Portsmouth Harbor and Piscataqua River

Deep draft channels 28 1,708,006Portsmouth Back Channel areas 3 900Little Harbor 2 176,609Rye Harbor 6 244,051Hampton Harbor and tributaries 27 819,142

Strafford CountyLittle Bay 1 556Great Bay and minor tributaries 1 15,000

Frequency and volumes of dredging at harbors in New Hampshire: 1950-1993 (NAI, 1994). TABLE 4.6

lobsters. Banner and Hayes (1996)mapped potential lobster habitat in GreatBay in 1996 using a suitability indexmodel, however, the lower estuarywhere lobsters are most abundant wasnot included in the study. Lobstersundergo a seasonal migration into theGreat Bay Estuary in late spring andmigrate well into Great Bay in the sum-mer and early fall. Migrating lobstersonly include lobsters at or near legal size,i.e., >40 mm carapice length. Many juve-nile lobsters overwinter in the lower Pis-cataqua River and the near coastal areaof New Hampshire. It is hypothesizedthat lobsters may take advantage ofaccelerated growth rates in the Great BayEstuary in summer (Dr. W. Watson, UNH,personal communication). Though juve-nile lobsters can be found in many habi-

tats from the shallow subtidal zone andin the deepest channel areas of the estu-aries, dive surveys and trap researchindicate that their preferred habitat isrock-cobble bottom (Dr. Hunt Howell,UNH and Mr. Bruce Smith, NH Fish andGame, personal communication).

The NH Fish and Game Lobster Pro-gram study areas for both juvenile andadult lobsters include the PiscataquaRiver south of Dover Point, the lowerriver, outer Portsmouth Harbor andcoastal area, and the Isles of Shoals. Seasampling data indicates that catch perunit effort (CPUE) from 1992 to 1996has been stable for all areas, with high-er catch rates in the river and coastalarea than at the Isles of Shoals (Figure4.6). Dive surveys indicate that lobstersare most abundant from June through

178

1992 1993 1994 1995 1996 1997Fish

Alewife 9,802 2676Cod 3,076,564 2,525,274 2,576,567 2,362,707 2,384,561 1,712,106Dogfish Spiny 402,184 1,641,614 2,597,792 2,106,255 1,079,522 1,009,140American Eel 285 1384Winter Flounder 125,714 85,869 80,684 63,729 61,857 30,429Hake Mix Red & White 23,231 8881 15,068 11294 30,295 36,629Atlantic Herring 562,413 774,292 435,200 56,775 33,655 152,431Pollock 1,028,452 1,082,602 886,582 745604 724,008 1,141,699American Shad 9,903 6549 28,226 30561 35,561 25,436Atlantic Silverside 8,888Smelt 36 346Tuna, Bluefin 146,042 102,881 110,654 83,716 85,203

Shellfish and WormsGreen Crab 3,515Rock Crab 24 118Lobster 1,529,292 1,693,347 1,650,751 1,834,794 1,632,829 1,166,068Mussels 115Sand Worms 599Sea Scallop 442 256 256 1,065Sea Urchins 102,494 46,163 12,117 4074 10,410 18,337Shrimp (Pandalid) 220,733 972,705 1,148,571 1,658,588 1,692,017 1,225,021

Totals*Landed Pounds 9,471,438 10,474,945 12,155,643 11,723,114 10,123,219 9,398,882Live Pounds 10,573,844 11,364,472 13,207,785 12,779,960 11,098,224 10,321,230

*Includes angler, bluefish, bonito, butterfish, crabs (Jonah, others) conchs, cunner, cusk, conger eel, flounder (Am. plaice, sand-dab, summer,witch, yellowtail), haddock, hagfish, silver hake, halibut, john dory, lumpfish, mackerel, menhaden, ocean pout, redfish, scup, sea raven,sharks, skates, squids, tautog, tilefish, yellowfin tuna, wolffishes.

TABLE 4.7 Recorded fish landings (landed pounds) in New Hampshire: 1992-1997.

179

October. Lobsters were sampled using anotter trawl in the Portsmouth Harbor areain 1991 and the data indicate that juve-nile lobsters are abundant (Johnston etal., 1994). The number captured per fiveminute tow at eight stations ranged fromthree to thirty three. Lobsters can also beplentiful in Great Bay at certain times ofthe year. Langan (1996) caught as manyas 26 juvenile lobsters per 10 minute towin the mid-Great Bay channel in July.

Lobsters and other marine organismsat sites outside Hampton Harbor havebeen monitored by NAI since 1975 aspart of environmental assessmentsdesigned to determine the impacts of theSeabrook nuclear power station. The sta-tion became operational in August, 1990,and data can be categorized as pre-oper-ational (1975-1989), operational (1991-

present) and 1990 data during the transi-tion. Nearfield sampling off HamptonHarbor (NAI, 1996) indicates that lobsterabundance has been stable since 1982,however 1995 CPUE of all lobsters (legaland sublegal) was higher than all previ-ous years. The high CPUE in 1995 couldbe related to elevated temperatures dur-ing 1995 (NAI, 1996). Changes in thelegal size limit in 1984, 1989 and 1990have resulted in a decrease in the cap-ture of legal size lobsters and an increasein the number of juvenile lobsters caught(Figure 4.7).

In 1996, an oil spill in the PiscataquaRiver had a negative impact on lobsters,particularly those that were in traps atthe time of the spill. An estimate of thenumber of lobsters killed from the oilspill is not available. A major rainstorm

1992 1993 1994 1995 1996 1997Fish

Alewife 4,900 576Cod 3,169,995 2,673,803 2,708,000 2,469,878 2,143,393 1,635,941Dogfish Spiny 50,638 252,983 393,548 397,812 189,537 145,723American Eel 430 2,076Winter Flounder 134,087 88,709 87,114 69,353 67,904 38,368Hake Mix Red & White 6,469 1,972 3,366 2,541 6,250 7,242Atlantic Herring 50,681 87,085 44,448 5,512 3,050 14,237Pollock 743,414 837,745 803,698 725,822 578,714 780,992American Shad 2,429 1,764 8,850 7,789 9,039 4,794Atlantic Silverside 4,616Smelt 43 395Tuna, Bluefin 1,208,612 1,299,083 1,231,522 1,197,550 849,403

Shellfish and WormsGreen Crab 1,177Rock Crab 13 60Lobster 5,033,198 5,567,109 5,566,282 6,655,660 6,563,641 4,636,975Mussels 12Sand Worms 2,138Sea Scallop 772 1,386 1,271 8,077Sea Urchins 49,589 26,501 6,648 3,359 11,604 16,870Shrimp (Pandalid) 252,492 932,247 818,524 1,420,581 1,274,983 1,047,257

Totals*Value ($) 12,054,527 12,941,155 13,397,832 14,925,401 13,531,968 10,500,781Landed Pounds 9,471,438 10,474,945 12,155,643 11,723,114 10,123,219 9,398,882

*Includes Angler, Bluefish, Bonito, Butterfish, Conchs, Crabs (Jonah, Others) Cunner, Cusk, Conger Eel, Flounder (Am. Plaice, Sand-Dab,Summer, Witch, Yellowtail), Haddock, Hagfish, Silver Hake, Halibut, John Dory, Lumpfish, Mackerel, Menhaden, Ocean Pout, Redfish, Scup,Sea Raven, Sharks, Skates, Squids, Tautog, Tilefish, Yellowfin Tuna, Wolffishes

Value ($) for recorded fish landings in New Hampshire: 1992-1997. TABLE 4.8

180

5

4

3

2

1

0July August September October

Coast

5

4

3

2

1

0July August September October

Shoals

5

4

3

2

1

0July August September October

Catch per Trap Setover DayRiver

19921993

19941995

1996

FIGURE 4.6 Comparison of sea sampled lobster catch per unit effort 1992-1996 (NHF&G Lobster Program).

181

May June July Aug Sept Oct

PreoperationalOperational

1995

Log10(x+1) Density

I II III IV

1.2

1.0

0.8

0.6

0.4

0.2

0.0

0.20

0.15

0.10

0.05

0.0

PreoperationalOperational

1995

Log10(x+1) Density

Stage

160

140

120

100

80

60

40

20

Lobster (legal and sublegal) Lobster (legal)

Lobster Larvae: Monthly Trends Lobster Larvae: Trends by Lifestage

PreoperationalOperational

1995

CPUEPreoperational

Operational1995

CPUE

June July Aug Sept Oct Nov June July Aug Sept Oct Nov

FIGURE 4.7Preoperational (1975/78-1989), operational (1991-1995) and 1995 means of: a. Weekly density (no./1000 m2) of lobster larvae at Station P2, b. Lobster larvae density by lifestage at P2, c. Monthly CPUE (15 traps) of total (legal and sublegal) lobsters at Station L1, and d.Monthly CPUE (15 traps) of legal-sized lobster at Station L1. Seabrook Operational Report, 1995.Vertical bars are 95% confidence limits.

in October, 1996 dumped up to 12” ofrain on the NH Seacoast on October 19and 20. The sudden drop in salinitykilled lobsters that were in traps as fardown the estuary as Portsmouth. Thetotal number of lobsters that succumbedto the massive freshwater input is notknown, although this may in part explainthe lower landed pounds and value forlobster in 1997 (Tables 4.7 and 4.8).

Other Commercial Fisheries

Other commercial fisheries in the GreatBay and Hampton/Seabrook estuariesinclude baitfishing for alewives, mummi-chogs (Fundulus sp.) and tomcod usinggillnets, seines and minnow traps; trap-ping for eels, and angling and dipnettingfor smelt. The landings and dollar valueof these fisheries in the estuaries are notknown, although limited data on thetotal catch of alewives, eels and smelt inNew Hampshire are presented in Tables4.7 and 4.8. There is also a commercialfishery for sea urchins, though this activ-ity takes place primarily outside the estu-aries in near coastal waters. Harvestmethods include SCUBA and trawlingwith an urchin sled. Concern by somethat the sled was disturbing bottom habi-tat prompted the NH Fish and Game toassess the impact caused by urchin drag-ging. Though the sled disrupted macroal-gae, they found that the sled had little

impact on nonvegetated hard bottom(Mr. Bruce Smith, NH F&G, personalcommunication). Thus, sleds can be usedanywhere seaward of the PiscataquaRiver bridges and outside of the otherNew Hampshire harbors. Theinshore/estuarine commercial scallopfishery was discussed in another section.It should be noted here that the inshore(>3 mi, < 25 mi) and offshore (>25 mi)groundfish populations have been insevere decline since the early 1980’s dueto overexploitation (NOAA 1992). Thereduced stocks and the strict regulationsimposed on commercial fishermen hashad a tremendous impact on coastaleconomies.

The commercial fishing fleet of NewHampshire also fishes in the Gulf ofMaine outside the estuarine environ-ment. The total recorded weight of fishlandings caught by the New Hampshirecommercial fishing fleet, and the value atthe pier from 1992 to 1997 are summa-rized in Tables 4.7 and 4.8, respectively,based on NMFS data. The landed poundshave declined somewhat from highs of12.1 million pounds in 1994, but areessentially the same as 1992 levels (Fig-ure 4.8). The value of the fish declined to$10.5 million in 1997, the lowest record-ed since 1992. Some of this may beattributed to the decrease in landings andvalue of lobsters in 1997.

182

1992 1993 1994 1995 1996 1997

Value in Dollars

Landings in Pounds

9

10

11

12

13

14

15

million

FIGURE 4.8 Total recorded fish landings and value in New Hampshire: 1992-1997 (NMFS).

183

The landings and values of twentyfinfish and shellfish species are listed inTables 4.7 and 4.8. The most consistentlyimportant species are lobsters and cod,both in terms of value and landings.Whereas the landings of lobsters hadbeen relatively constant until 1997, thecod landings have declined steadily since1992, from 3.1 million to 1.7 million land-ed pounds (Figure 4.9). A similar trend isapparent for winter flounder (Figure4.10). However, other species have exhib-ited different trends. The landings of spinydogfish increased dramatically from 1992

to 1994, then declined sharply until level-ing off after 1996 (Figure 4.9). Shrimplandings exhibited a steady increase from1992 to 1996 (Figure 4.9). Sea urchin land-ings declined sharply from 102,494pounds in 1992 to 4074 pounds in 1995,with a slow rebound since (Table 4.7).Other trends are also apparent, and theseall reflect changes in world market prices,harvest pressure, government regulationsand abundance of wild stocks. For exam-ple, the value of the lucrative tuna fisherywas adversely affected in 1998 by theAsian financial crisis.

1992 1993 1994 1995 1996 1997

million

.5

1.0

1.5

2.0

2.5

3.0

3.5

0

Recorded Landings in Pounds

CodSpiny Dogfish

Shrimp

Recorded landings of cod, spiny dogfish and shrimp in New Hampshire: 1992-1997 (NMFS). FIGURE 4.9

1992 1993 1994 1995 1996 1997

Thousand

20

40

60

80

100

120

140

0

Recorded Landings in Pounds

Recorded landings of winter flounder in New Hampshire: 1992-1997 (NMFS). FIGURE 4.10

Aquaculture

Though aquaculture is one of the fastestgrowing industries in North America andglobally, it has been slow to take hold inNew Hampshire. In the early 1980’s therewere four commercial shellfish aquacul-ture operations in the Great Bay Estuary,engaged in the culture of indigenous(Eastern) oysters, the European flat oys-ters and hard clams (Mercenaria merce-naria). Three of these operations werelocated in New Hampshire and one inMaine, and only the Maine company isstill in operation in 1998. Failure of thestate shellfish sanitation program to meetthe requirements of the National ShellfishSanitation Program (NSSP) resulted inclosure of all commercial marine aqua-culture operations in New Hampshire bythe U.S. Food and Drug Administration(USFDA) in 1989, and the three NH com-panies were forced to cease operations.To date, New Hampshire has beenunsuccessful in gaining endorsement ofits growing waters program (NSSP, 1995)from the USFDA, though the State’s shell-fish sanitation program has improved inrecent years.

In 1996, a commercial oyster aqua-culture permit was granted to three com-mercial fishermen participating in aresearch program associated with UNH.The project was funded by theNOAA/NMFS Fishing Industry GrantsProgram which was created to providecommercial fishermen with alternativebusiness opportunities. The project pro-duced nearly 730,000 oyster seed in1996, which were planted at a five acresite near the mouth of the Oyster River inLittle Bay. The project has continued tothe present. The same program(NOAA/FIG) has funded a fisherman toresearch sea urchin culture, and com-mercial permits were granted to him in1996, and to another individual in 1997.One of these operations was located inHampton Harbor.

Other activity in shellfish cultureincludes a UNH sea scallop researchproject which is evaluating culture andstock enhancement techniques for scal-lops and several UNH sea urchin proj-

ects. In 1998, Spinney Creek Shellfish Co.in Eliot, ME, began operating a softshellclam hatching facility and successfullyproduced seed for outplanting experi-ments in flats on the Maine side of theGreat Bay Estuary. UNH CooperativeExtension has also operated a culturefacility for softshell clams in Seabrook.The facility is primarily used for 4H edu-cational programs.

There has also been a great deal ofactivity in the past few years associatedwith finfish culture. A commercial sum-mer flounder hatchery and nurserybegan operation in 1996. The company,Great Bay Aquafarms, is currently pro-ducing fingerlings for growout at otherlocations but plans to construct agrowout facility on site in the near future.The company’s operations are based in awarehouse on the PSNH power genera-tion site in Newington, NH and areentirely indoors, using sophisticatedrecirculating and biofiltration technologyto grow fish in land based tanks. It is thefirst commercial summer flounder opera-tion in the U.S. More than 250,000 fishwere produced in 1996. Research onlumpfish, several flounder species, codand haddock is being conducted at theUNH Coastal Marine Laboratory. Engi-neering research on offshore fish penshas been conducted in association withone of the finfish projects by the UNHOcean Engineering Department.

New Hampshire has the opportunityto develop a viable aquaculture industry.As far back as the 1940’s Professor C.Floyd Jackson recommended developingaquaculture of clams and oysters in GreatBay (Jackson 1944). Ayer et al. (1970)determined that a seed oyster industry inGreat Bay could be viable if hatcheryreared seed were used. More recently, aNH legislative study committee on aqua-culture (NH Legislative Committee, 1993)recommended development of an oysterculture industry. Research and develop-ment in other parts of the country andabroad have resulted in technologies thatare suitable for New Hampshire. Thereare opportunities in the high technology,land-based finfish operations similar toGreat Bay Aquafarms, as well as in envi-

184

185

ronmentally friendly and ecologicallybeneficial shellfish culture. Mussels, scal-lops, oysters, clams and seaweeds are allexcellent candidates for culture in NewHampshire and would provide econom-ic as well as ecosystem benefits. Aqua-culture could provide a means ofmaintaining seafood production in theNew Hampshire Seacoast, and providethe beleaguered fishing industry with analternative to harvest fisheries. A recentUNH Sea Grant Document (Howell et al.,1997) outlines the potential and benefitsof aquaculture development in NewHampshire.

4.3.1.4 Marine Products

The NAI (1994) report identified threeseafood processing facilities in NewHampshire. The Yankee Fisherman’sCoop Pier in Hampton Harbor handlesboth shellfish and finfish, the PortsmouthFish Co-op handles groundfish and LittleBay Fisheries in Portsmouth Harbor han-dles lobster.

4.3.1.5 Marine Plant Harvesting

Salt hay farming continues to this dayand has experienced a small revival innorthern Massachusetts, yet the impactsfrom salt hay farming on salt marshecosystems are unknown (Rozsa, 1995).Algae have been harvested for varioususes in New England, but such harvest in

New Hampshire estuaries are poorlyknown and probably minimal. Impactsto the algal resources from experimentalharvesting have been assessed for thered alga, Irish moss (Mathieson andBurns 1975). They found that plantscould recover in a year after carefullycontrolled harvesting, but winter harvest-ing had greater impacts to the algal beds.Seagrass has been harvested in the north-east for building insulation and uphol-stery stuffing, but it is probably mostwidely used, as wrack collected fromshorelines, for garden mulch and fertiliz-er. The scale of such activities in NewHampshire does not appear to havebeen large, and although their potentialimpacts are unknown, they are likelyminor.

4.3.2 RECREATIONAL USES

4.3.2.1 Tourism Economics

Tourism and travel are important to theSeacoast economy (Okrant et al., 1994).Statewide in FY 1992, 10.3% (57,740) ofall jobs were directly dependent on trav-el/tourism, and associated payrollstotaled $770 million, or 4.8% of all NewHampshire payrolls. In the Seacoast, 16%of the region’s jobs were supported bytourism (Figure 4.11). Monthly spendingfor rooms and meals in the Seacoast dur-ing the six months from May-October

Statewide WhiteMountains

LakesRegion

Dartmouth-Lake Sunapee

Seacoast MerrimackValley

Monadnock

17.7

31.4

25.7

17.115.3

11.610.1

Percentage of jobs supported by travel and tourism in New Hampshire regions in 1992 FIGURE 4.11 (Okrant et al., 1994).

was higher than during November-April,with a peak spending of >$20,000,000 inAugust.

There are numerous tourist-relatedactivities in the Seacoast that involve useof charter boats. These activities includesport fishing, whale watching, windjam-mers/charter sailing, and harbortours/day cruises. The numbers of ves-sels involved with these activities andtheir locations in the Seacoast are sum-marized in Table 4.5. None of the vesselsare located in the tidal rivers, with a rel-atively even spread of locations for thedifferent activities across the Seacoast.

4.3.2.2 Boating and Related Activities

The State of New Hampshire Departmentof Safety records boat registration andprovides annual summaries. Boats arerecorded by size, hull material and type(inboard, outboard, etc.). No differentia-tion by tidal and freshwater use is pro-vided. A survey by NAI (1994) of harbor

officials in New Hampshire showed8,522 and 341 recreational vessels oper-ated during 1992 in Rockingham andStrafford counties, respectively (Table4.9). The NHDES used 1993 NH Depart-ment of Safety data to estimate that 3,468vessels were tidal water registrations hav-ing marine sanitation devices.

Of the 8,863 total recreational ves-sels in 1992, 335 were at slips and 738 atmoorings (Table 4.9). There were alsonine marinas or yacht clubs in Rocking-ham County, plus four in Strafford Coun-ty. In 1995, the NHDES counted ninemarinas/yacht clubs. The New Hamp-shire Port Authority has authority overmoorings. Permits are granted for moor-ings at 22 sites. Waiting lists are main-tained for moorings at the different sites,with as many as 211 people waiting forLittle Harbor moorings in December,1996, and an estimated 20 years wait atRye Harbor. Mooring holders are classi-fied as resident and non-resident, as well

186

Recreational VesselsSite* Total No. at slips at moorings

RiverSquamscott R. 80 15 4Lamprey R. 45 30 14

Lamprey River Marina 30 30 0Oyster R. 41 0 41Cocheco R. 50 30 4

George’s Marina 30 30 0

Harbor/BayGreat Bay 7 0 7Little Bay 500 130 248

Great Bay Marina 158 100 58Little Bay Marina 50 30 20

Portsmouth Harbor 7500 40 140Portsmouth Yacht Club 25 20 5Kittery Yacht Club 26 20 6

Portsmouth Back Channels 30 0 30Little Harbor 330 160 120

Wentworth Marina 160 160 0Hampton Harbor 280 50 130

Hampton River Marina 150 40 110

Total 8863 445 738

Rockingham County 8522Strafford County 341

*Sites include 13 marinas, 9 in Rockingham County and 4 in Strafford County.

Private recreational vessels in coastal New Hampshire in 1992 (NAI, 1994).TABLE 4.9

187

as mooring either pleasure or commer-cial boats. In 1991, there were 1390mooring permits sold (Figure 4.12). Therapid increase from 1976 to 1991 leveledoff after the NHPA adopted and imple-mented a harbor management plan in1989. Mooring field parameters are set bythe US Army Corps of Engineers, andcurrent space for new mooring permits isextremely limited. In 1996, the areas withthe most permits were Little Bay (222),Hampton (193), Little Harbor (131), Rye(129) and the Piscataqua River (119),with 268 permits spread around eightspecific areas in Portsmouth Harbor, theBack Channel and other areas inPortsmouth. Very few new permits areexpected in the near future.

Another means of assessing boatingactivity can be found in data from theNew Hampshire Bridge Authority foropenings at the Memorial Bridge inPortsmouth. The openings are a measureof traffic for vessels greater than 11 feet

in height, and include sailboats, com-mercial tugs, barges, freighters and manypleasure craft. The monthly and annualcounts for boats under the bridge from1989 to present are shown in Figure 4.13.Recently there has been a slow, steadydecrease in traffic, from 7470 in 1990 to5860 in 1996. Figure 4.13 shows that thegreatest traffic occurs during the summermonths of July and August, whereas thelightest traffic occurs during wintermonths.

4.3.2.3 Recreational Fishing

The Great Bay Estuary supports a diversecommunity of resident, migrant, andanadromous fishes, many of which arepursued by recreational fishermen.Recreational fishermen mainly pursuestriped bass, bluefish, salmon, eels, tom-cod, shad, smelt, and flounder. Fishing isnot limited to boat access, as cast or baitfishing is done from the shore in manyplaces, from the bridges crossing the

Number Sold per Year

19951994199319921991199019891988198719861985198419831982198119801979197819771976 19960

100

200

300

400

500

600

700

800

900

1000

Annual mooring permit sales by the New Hampshire Port Authority: 1976-1996. FIGURE 4.12

FIGURE 4.13 Monthly and annual vessels passing under the raised span of the Memorial Bridge, Portsmouth, New Hampshire: 1989-1996.

estuary, and ice fishing is popular in thetidal rivers. Recreational fishing in saltwater does not require a license exceptfor smelt in Great Bay Estuary; trout,shad and salmon in all state waters; andto take any fish species through the ice.

The yearly New Hampshire Recre-ational Saltwater Fishing Digest (NHF&G,2000) provides profiles of the eight pri-mary game fish species: striped bass,bluefish, Atlantic mackerel, rainbowsmelt, winter flounder, Atlantic codfish,haddock and pollock, as well as profileson twenty other game fish species thatmay be found in coastal New Hamp-shire. The digest also provides informa-tion on the ethics of recreational fishing,the ‘Let’s go Fishing’ program, safe boat-ing, a list and maps of coastal accesssites, instructions on catch and releasetechniques, proper digging of clams andrequirements for recreational lobstering.

Several charter boat companies inthe Great Bay Estuary take fishermen to

pursue striped bass, bluefish, and pol-lack, while companies operating out ofHampton Harbor carry fishing parties toinshore waters for clams and to the off-shore waters to pursue cod, flounder,mackerel, and other fish. One of themajor winter activities in Great and LittleBays is ice fishing for smelt. The smeltfishery in Great Bay occurs primarily inthe Greenland Cove and the Lamprey,Squamscott and Oyster river areas fromearly January to March. Numerous busi-nesses cater to smelt anglers, and accesssites for smelt fishing are available. TheNHF&G Department has pursued stock-ing and monitoring efforts on selectedfish stocks (e.g., shad and Atlanticsalmon; see section 4.4.3.1: AnadromousFish Restoration) in order to enhancerecreational fisheries (NHF&G, 1989).Another important recreational fishingactivity is trap fishing for lobsters. Almost150 recreational lobstermen set trapsthroughout the Great Bay and Hamp-

188

1990

1992

19941996

JanFeb

MarApr

MayJun

JulAug

SeptOct

NovDec

Total Number ThroughRaised Bridge Span

5166

7,74

0

5,94

8

6,55

1

6,18

4

6,14

2

6,09

1

5,86

0

189

ton/Seabrook estuaries, with thePortsmouth Harbor area being a ratherpopular location.

Studies by NHF&G Department con-sultants identified substantial sums ofmonies spent on marine recreationalfishing. An estimated 88,000 saltwateranglers spent over $52 million dollars in1990 on fishing-related activities(approximately $600 per person). Thelargest expenditures were for food andbeverages, automobile fuel, charter/partyboat fees, bait and fishing tackle, andboat fuel. A substantial amount of thattotal is estimated to come from expendi-tures in Great Bay estuarine activities.More information on recreation fishing ispresented in the Living Resources section(see Striped Bass, 3.2.1.1).

4.3.2.4 Shellfish Resource Management and Recreational Harvesting

Shellfishing is an important and popularrecreational activity in the estuaries. TheGreat Bay Estuary supports a large recre-ational shellfishery for oysters, clams andmussels. Oysters are the predominantshellfish resource utilized in Great Bay,although Little Harbor supports moreconcentrated populations of clams. Majoroyster beds are located in Great Bayproper, as well as in the Piscataqua, Bel-lamy, and Oyster rivers, with scatteredpockets of oysters also found throughoutthe estuary (Figure 1.7). Though onlyrecreational harvesting is allowed, theestimated dollar value of oysters in majorbeds was nearly $1.6 million in 1981 and$3 million in 1994. Approximately 5,000bushels of oysters, valued at $300,000 areharvested annually by the 1,000 licenseholders (Manalo et al., 1991). Recreation-al harvesting of shellfish in the Great BayEstuary is currently limited to most ofGreat Bay and Little Bay, with the Pis-cataqua River (including Little Harbor),and the smaller tidal rivers closed to har-vesting due to bacterial pollution (Figure1.8). The harvesting of softshell and razorclams in Great Bay, though difficult,became intensified in recent yearsbecause of limitations on harvesting ofmore popular clamming areas such as

the flats in Hampton and Little harbors. The principal shellfish resource in

Hampton Harbor is the softshell clam,found in five major resource areas (Fig-ure 1.9). These flats were closed in 1988,but with the conditional reopening ofsome of the flats in the fall of 1994 andfurther openings in 1998, almost 3,000clamming licenses were sold in 1994 (upfrom 239 licenses in 1993). Prior to clambed closures in 1988, the average num-ber of licenses sold in the State between1971-1987 was 6,400. Rye Harbor clamflats remain completely closed (Figure1.11). The contribution of recreationalshellfishing in Hampton Harbor to thelocal and state economy has been esti-mated to be $3 million per year (Manaloet al., 1992).

Effects of Classification on ShellfishResource Productivity

Resource productivity of shellfish beds isdetermined by management of harvest-ing pressure and by the natural mortali-ty, reproductive capacity and recruitmentof the shellfish themselves. Causes ofnatural mortality include predation, dis-ease, and siltation (in the case of oys-ters). Recruitment (addition of newindividuals) depends on reproductivesuccess, larval survival and successfulmetamorphosis. Classification of shellfishgrowing areas, which determines whereshellfish can be harvested, plays animportant role in shellfish resource pro-ductivity.

Oysters thrive in lower salinitywaters than other important species ofshellfish, and therefore are often foundnear sources of freshwater inflow such astidal rivers. The locations of major oysterbeds have been described in severalpublications dating back to the 1940’s(Jackson 1947, Ayer et al 1970, Nelson1981) and the current locations of bedsare shown in Figure 1.7. Due to theirproximity to pollution sources and asso-ciated higher than acceptable levels offecal bacteria, all oyster beds in the Bel-lamy, Oyster, Piscataqua and SalmonFalls rivers, as well as those in southwestGreat Bay have been closed since 1989,and some have never been open to

direct harvest. In a turbid estuary likeGreat Bay, undisturbed (unharvested oruncultivated) oyster beds tend to accu-mulate silt which can result in burial inareas with low current velocities, and inimpairment of larval attachment becauseof a lack of clean substrate even in bedswith high flows. MacKenzie (1989) foundthat even a millimeter of silt on an oystershell can deter larval settlement. Theaction of harvesting, whether by tongs ordredge, or cultivation with some sort ofmechanical device, helps to remove silt,expose buried shell and provide a favor-able substrate for larval settlement. Astudy conducted in 1991 (Sale et al.1992) found that oyster beds at NannieIsland and Adams Point which are har-vested recreationally with tongs andrakes, and beds on the Maine side of thePiscataqua River which are harvestedwith a small hand drag, showed majordifferences in population structure thanbeds in the Oyster River and on the NewHampshire side of the Piscataqua Riverwhich had been closed to harvest. Theharvested beds showed higher relativedensities of smaller oysters indicatingbetter recruitment, while the populationsin closed areas were skewed towardlarger, older individuals. These findingsare well supported in the literature(MacKenzie 1989, Visel 1988). Lack ofharvesting and cultivation in some of theoyster beds in the Great Bay Estuary hasprobably contributed to significant lossof oyster areal coverage and density inthe Oyster, Bellamy, and Piscataquarivers and in southwest Great Bay(NHF&G, 1991).

Closure of the clam beds, and result-ing absence of harvest pressure can havevariable effects on clam populations.Besides the depletion of approximately80% of adult clams, standard diggingpractices can reduce juvenile clam densi-ty by 50% through physical damage andexposure to predators (NAI, 1996). Onthe other hand, harvesting, which causesa change in sediment density and tex-ture, can enhance settlement of larvalMya. Also, when tidal flat areas areundisturbed, blue mussels can formdense beds, sometime up to a foot thick,

that can prevent settlement of clam lar-vae. In Hampton Harbor, closure of allflats in 1989 resulted in an overallincrease in clam density, indicating thatrecreational clam digging was a signifi-cant source of mortality from adult andjuvenile clams prior to April 1989 (NAI,1996). The changes in clam density,however, varied from flat to flat. From1990-1995, adult clam densities quadru-pled in the middle ground, while Com-mon Island densities did not change, andHampton River density decreased by50%. The effect of clam digging on theCommon Island and Browns River flats,which reopened in 1994, was not appar-ent in 1995, as clam densities were simi-lar in the two years. Though predation,disease and spatfall play a major role indetermining clam densities in HamptonHarbor, a report by Savage and Dunlop(1983) clearly demonstrates the effect ofclam digging on clam populations.Therefore closure of areas, whether forresource management or public healthreasons, generally results in greater den-sity of adult and juvenile clams.

Harvesting Effects on Other Wildlife

Though there is general agreement inshellfish producing states that oyster andsome types of clam harvesting improveshellfish productivity (Visel 1988,MacKenzie 1989, Rask 1986) and do notharm benthic or pelagic species, thereare few scientific studies that have dealtspecifically with the effects of oyster har-vesting on benthic populations. Dumb-auld (1997) reviewed a number ofstudies of the impact of oyster cultureand harvesting on benthic communitieson the west coast of the U.S. and con-cluded that mechanical harvesting hadno long term effects on benthic popula-tions. Langan (1995) found no differ-ences in density or species diversity ofbenthic invertebrates between an unhar-vested oyster bed in the Piscataqua Riverand one which was harvested with atowed hand drag.

There have been no documentedadverse effects of scallop dredging onbenthic populations, though Caddy(1973) reported damage to juvenile and

190

191

adult scallops by a large, heavy offshorescallop dredge. It is unlikely that thesmaller sized dredges used for inshorescalloping in New Hampshire cause thesame magnitude of damage.

The effect of clam digging on under-sized clams was discussed earlier, andthere have been no documented studiesof effects of clam harvesting on otherwildlife in Hampton Harbor.

Siltation and Harvesting Effects

The effect of siltation on unharvestedoyster bed productivity was addressed inan earlier section. It is reasonable toassume that mechanical or even handharvesting of oysters will release sedi-ment into the water column. No studieshave been done in the Great Bay Estuaryto assess the impact of resuspended sed-iments from oyster tonging, however,Langan (1995), measured suspendedsediments in the track of a towed oysterdrag on a Piscataqua River oyster bed.Water samples were taken with a sub-mersible pump approximately 0.25 mfrom the bottom every 20 meters for adistance of 110 meters of the drag track.Ambient suspended sediment concentra-tion was 10 mg/L. This concentrationincreased to 22 mg/L at a 10 m distancebehind the drag and gradually decreasedwith distance before returning to ambi-ent conditions at a distance of 110meters. The study indicates that the dis-turbance of a towed drag is localized andsuspended sediment conditions quicklyreturn to ambient levels.

Though sediment disturbed by clamdigging undoubtedly results in someresuspension of sediments when the tidebegins to cover the clamflats, there hasbeen no documentation in New Hamp-shire of adverse effects of resuspensionfrom clam digging.

Management Strategies for Recreational Beds and Flats

Management strategies for recreationaloyster beds consist of a daily harvestlimit of one bushel of unshucked oystersper day per license holder, and a closedseason in July and August. Oyster licens-es may only be obtained by New Hamp-

shire residents, and harvesting may onlybe done between sunrise and sunset byhand, rake or tong. The license must bedisplayed on the container and oystersmay not be shucked on site. Areas opento harvest are determined by the NHDepartment of Health and Human Ser-vices and area closures are enforced bythe NH Fish and Game Law Enforcementdivision. Oyster densities and sizes aremonitored periodically by the MarineFisheries Division of the New HampshireFish and Game. The recreational harvestis not recorded, therefore it is difficult toassess the effect of harvesting on oysterpopulations. Ayer (1970) estimated thatannual harvest in the late 1960’s to beapproximately 3,000 bushels. An oystersurvey by Manalo et al. (1991) estimatedthe harvest to be about 5,000 bushelsbased on responses from one third oflicense holders. A 1997 survey by NHFish and Game estimates an annual har-vest from 1993 to 1996 of approximately3,000 bushels. Recreational license sales,which had been stable for may years atabout 1000 licenses, declined to <800licenses in 1996.

Recreational oyster management hasalso included an enhancement programundertaken by NH Fish and Game (Nel-son 1989). Approximately 1000 bushelsof surf clam shell were planted near Nan-nie Island and 500 bushels at AdamsPoint on firm bottom sparsely populatedby oysters. Spatfall on the clean surf clam(238/m2) was significantly higher thanon existing shell (8.2/m2). The projectdemonstrated that shell planting is aneffective means of enhancing oyster pop-ulations. It should be noted that in highsediment areas, surf clam shells act simi-larly to sediment collectors as theyalmost always land cup up and fill withsediments, thereby reducing their effec-tiveness in catching oyster spat overtime. Experiments with different types ofshell as a spat attractant (Ayer 1970, Lan-gan 1996) indicate that oyster shells andscallop shells are more effective.

Commercial harvest of clams in NewHampshire ceased in the 1950’s. Regula-tions for management of softshelledclams have changed considerably over

the years, with recreational harvestingbecoming more restrictive in order toprotect the resource. Clamming is per-mitted in daylight hours on Friday andSaturday from the day after Labor Day toMay 31, with Hampton/Seabrook Harborflats not opening until November 1.Clammers must have a valid license,available only to New Hampshire resi-dents. Daily limit is a 10 quart pail ofunshucked clams. The clam harvest hasbeen estimated by head counts of clamdiggers. During the period 1980-1982, ata time when there were 5,000 to 6,000licenses, it was estimated that the annualharvest ranged from 2,000 to greater than6,000 bushels (Savage and Dunlop 1983),though some documents report as manyas 16,000 bushels harvested in the early1970’s. With the current rainfall condition(< 0.1 “ of rain in the preceeding fivedays, except <0.25 “ during Decemberthrough March, or any occurrence of>0.1” rain in 24 h), the reduced season inHampton Harbor, and fewer licensessold since the 1989 closure, it can be sur-mised that current harvest is lower thanthe in previous 80-82 years. License salespeaked at nearly 14,000 in the 1975,dropped to less than 300 in the early1990’s and have rebounded in 1994-1996due to the reopening of Hampton Har-bor. During the 1996-97 clamming sea-son (November 8, 1996 to May 30, 1997)in Hampton Harbor, clamflats were openfor 19 days, during which an estimated900 bushels of clams were harvested byan estimated 2,880 recreational har-vesters (NHF&G, 1997b).

A clam enhancement study wasundertaken by the New Hampshire Fishand Game in 1988 on the Willows clamflat in Hampton Harbor (Nelson 1989).Approximately 30,000 seed clams wereplanted at a density of 15 spat/m2 underpredator exclusion netting, and at 3.4spat/m2 in an adjacent area. Additionalnetting was placed on the flat to protectany natural spat that might settle. A littleover two months after planting, the areawas sampled and only two seed clamswere recovered. It was determined thatnatural spatfall was very poor and that

the planted clams either moved or wereeaten by predators.

Illegal Harvesting

Illegal harvest of clams occurs in theHampton/Seabrook Estuary. Over thepast several years, there have beenarrests to discourage illegal harvest.However, the activity, which is conduct-ed under cover of darkness, is very lucra-tive and difficult to control, even thoughlaw enforcement is also concentrated onnighttime activity. Removal of largequantities of clams by illegal commercialdigging presents a problem for resourcemanagement, and represents a publichealth threat if the clams are harvestedfrom closed areas and sold to an unsus-pecting public. Illegal harvesting ofclams, oysters and other shellfish in otherareas has not been documented.

Post-harvest Processing

The University of New Hampshire has along history of scientific studies on post-harvest processing of shellfish to removemicrobial pathogens. In addition, the exis-tence of Spinney Creek Shellfish, Inc.(SCS), a commercial shellfish facility inEliot, ME, has provided an excellentvenue for scientific and applied studies onthe post-harvest processing of shellfish.The potential for contamination problemsin each step of their process has beenevaluated (Howell et al., 1995). The effec-tiveness of ultraviolet depuration on oys-ters, clams and mussels has beenconfirmed at SCS and in laboratory-scaledepuration tanks (Jones et al., 1991a&b;Panas et al., 1986). Although depuration isnot effective for removing pathogenic vib-rios from shellfish (Jones et al., 1991a&b),relaying shellfish into unfiltered estuarinewater that does not contain pathogenicvibrios has been effective in reducing vib-rio levels to low levels (Jones et al., 1995).Viruses are also generally resistent toremoval via traditional depuration. Cur-rent research is underway at UNH/JEL todetermine the potential for depuration ofthe human parasites Cryptosporidium andGiardia spp. (Dr. S. Torosian, personalcommunication).

192

193

4.4.1 BASE PROGRAM ANALYSIS

The following sections review the tech-nical information that is available for var-ious aspects of issues related tomanagement of human uses of NewHampshire’s Seacoast. Another NHEPdocument, the Base Programs Analysis(Carlson, 2000), reviews existing local,state and federal regulatory measuresand natural resource management oreducation programs which impact estu-arine resources. Thus, those topics arenot included in this document.

4.4.2 LAND PROTECTION

The percentage (16%) of permanentlyprotected land within 300 feet of theshoreline of New Hampshire’s tidalwaters (Figure 4.4) is significant in that amuch lower percentage of shoreland isavailable for development than in inlandareas. Much work to prioritize land areas,based on evaluation of habitat value, hasbeen completed.

Various strategies have been used tohelp identify and prioritize important

habitat areas in coastal New Hampshire.Important habitats in coastal New Hamp-shire have been identified using a GIS(Sprankle, 1996). All habitat was rankedbased on the habitat requirements of 55species of concern. Ranks were summedfor all species and habitats potentiallyimportant for the target species weremapped. In a related effort, New Hamp-shire’s most important natural resourceswere identified (Ueland et al., 1995). TheSeacoast and Great Bay were identifiedas high priority areas, based on the valueof their natural resources. The GIS mapsinclude a delineation of important natu-ral resources and habitats. Banner andHayes (1996) conducted a pilot study incoastal New Hampshire to developmethods for selection of evaluationspecies, assessing habitat suitability andmapping habitat, as well as to identifyand facilitate protection of importanthabitats using that information. Theymapped the habitats for 25 species thatwere selected based on local concernsand a species priority list for the Gulf ofMaine.

4.4

MANAGING HUMAN USES

GIS Surveying in process

4.4.3 HABITAT RESTORATION AND MITIGATION

Human development and pollution ofestuaries and coastal areas has led to thedestruction of important habitatsthroughout the world. Though NewHampshire’s estuaries are in good condi-tion relative to many other estuaries onthe east coast of the U.S., human activi-ties that occurred prior to the realizationthat natural habitats play an importantrole in the ecology and economy of theregion have resulted in impacts to impor-tant estuarine habitats. Many tidal marsh-es have been filled and tidal flowrestrictions caused by road constructionhas degraded others. Dams constructedon tidal rivers prevent passage ofanadromous fish. Sediment erosion fromclearcutting, and sawdust from lumbermills has smothered some shellfish beds,while historical direct dumping and dis-charge of untreated industrial and munic-ipal waste has contaminated others.Though the regulatory framework forprotecting further habitat destruction hasbeen established, restoration of habitatsthat were destroyed or adversely impact-ed by past activities has been and willcontinue to be a priority in New Hamp-shire’s estuarine and coastal areas. Overthe past two to three decades, the devel-opment of techniques for habitat restora-tion has made the prospect of restoringor creating habitats a viable option forcoastal resource management.

A mitigation process is required infederal regulations for major develop-ment projects that impact legally protect-ed environments (e.g., wetlands). Theregulation requires three steps: investiga-tion of alternative sites, reduction of theproposed impacts, and compensatoryaction to replace the functions and val-ues of the habitats to be impacted by thedevelopment. When estuarine or coastalhabitats are involved in such a develop-ment, habitat restoration is the preferredmechanism of compensatory mitigation.

4.4.3.1 Anadromous Fish Restoration

During the industrial development peri-od in the 18th and 19th centuries, dams

were constructed on nearly all of NewHampshire’s tidal rivers. The dams pre-vented access by anadromous fish totheir freshwater spawning grounds.Beginning in the 1970’s, fishways or fishladders were constructed on theCocheco, Lamprey, Oyster, Taylor, Win-nicut and Exeter rivers (Figure 4.14). Thefishways now allow passage of river her-ring, shad, lampreys and many otherspecies from tidal to fresh waters tospawn.

Currently, the NH Fish and GameDepartment is maintaining fishways andmonitoring the spawning runs of severalspecies. They are also working to restoreanadromous fish populations throughtheir Coastal Anadromous Fish SpeciesProgram. The goals of this programinclude raising sea-run salmon for stock-ing coastal rivers; the transfer of spawn-ing shad into coastal rivers; andconstruction of fish passage systems.Approximately 250,000 salmon fry werestocked into the Lamprey and Cochecorivers with the help of 50-100 volunteersin 1996 and 1997 (Cornelisen, 1998), apractice that has occurred yearly sincethe 1980s. Ongoing NHF&G monitoringis tracking the progress of these effortsand provides valuable data on numbers,size, sex and age of returning fish popu-lations.

4.4.3.2 Shellfish Restoration

Restoration of degraded or depletedshellfish beds has become a major focusin the United States and abroad. There isnot only an economic incentive, but anecological one as well. Areas that havelost the majority of their shellfishresources (Chesapeake Bay, DelawareBay) are experiencing severe water qual-ity problems due to a large extent to theloss of filter feeders. Oysters in theChesapeake Bay in 1900 were capable offiltering the entire water volume of thebay in 24 hours. The reduced number ofoysters (due to disease and overharvest-ing) would now take nearly a year to fil-ter the same volume.

The application of techniques devel-oped by the aquaculture industry hasmade restoration of natural oyster beds

194

195

WatsonWaldron Dam

Cocheco River

Oyster River

LampreyRiver Dam

WinnicutRiver Dam

ExeterRiverDam I

Taylor RiverPond Dam

PickpocketDam

FIGURE 4.14

Fish ladders in the New Hampshire

Coastal region.

possible. Shell planting (described in sec-tion 4.2.1.4), remote setting using hatch-ery reared larvae and construction ofartificial and shell reefs have all provensuccessful in oyster restoration. In areaswhere oyster diseases are present, resist-ant strains of oysters may be introduced.An aquaculture project by researchers atUNH/JEL which began in 1996 to deter-mine whether oyster aquaculture is a fea-sible alternative for commercial finfishharvesters has employed remote settingof hatchery reared larvae on natural andartificial cultch. Good results wereobtained using French spat collectorscalled “Chinese hats”, and 130,000 spatwere produced on 30 Chinese hat unitsand planted in the fall of 1996. An addi-tional 600,000 spat set on shell were alsoplanted. Growth and mortality of theoyster seed is being monitored, and asecond year of setting commenced inMay, 1997. These same techniques canbe used to restore public recreationalbeds. In addition, oysters in suspendedculture can be used to filter phytoplank-ton from waters such as the Salmon FallsRiver where intense blooms occur insummer. A current UNH project hasestablished two new oyster beds in theSalmon Falls River and will determinebeneficial impacts on water quality.

Softshelled clam restoration is notquite as advanced as oyster restoration. Apast restoration effort was described insection 4.2.1.4. A number of techniques

ranging from planting hatchery rearedclams to manipulating the flats toenhance natural settlement have metwith mixed success. There are severaltechniques that have been used in Maineand Cape Cod that have shown excellentresults (Beal 1994; Leavitt, personal com-munication; Gowell, personal communi-cation).

Though the amount of estuarinehabitat suitable for sea scallops is small,sea scallops are an important winter fish-ery for some NH lobstermen and anactive recreational fishery for SCUBAdivers. Sea scallop beds are located atthe mouth of Portsmouth Harbor fromSalamander Point to Fort Point near FortMcClarey, in Spruce Creek and from FortPoint to Jaffrey Point along the New Cas-tle shore. Density, size (age) distributionand movement of scallops was studiesby Langan (1994) in the lower PiscataquaRiver. In 1996, artificial spat collectorswere deployed in the river to test the fea-sibility of spat culture and naturalenhancement using non-destructivemethods to collect natural scallop spat.Similar techniques are practiced in Cana-da, New Zealand and Japan. These meth-ods form the basis of sustainablecommercial scallop fisheries in thosecountries, and have been shown toenhance natural populations by increas-ing recruitment in the vicinity of the col-lectors. Spat settlement in the area underthe collectors were monitored in June,

196

Spat collectors

R. L

AN

GA

N

197

1997, and compared to adjacent areas todetermine the effectiveness of the collec-tors for enhancing natural populations.

4.4.3.3 Saltmarsh Restoration

Restoration of many salt marshes inNew Hampshire has focused onreestablishment of tidal exchange tomarshes where tides have been restrict-ed by undersized and damaged culverts(Drakeside Road Marsh, Locke RoadMarsh), water control structures such asflap gates (Mill Brook Marsh StuartFarm), and berms of debris or dredgespoil (Awcomin Marsh in Rye Harbor,Sandy Point Marsh at Great Bay NERR)(Morgan et al., 1996). Reestablishmentof tidal regimes similar to those founddownstream of the restriction has result-ed in rapid recovery of several functionsand successful restoration projects (Bur-dick et al., 1997). Restoration activitiesat 6 restrictions has improved tidalflooding to approximately 60 acres ofimpacted salt marshes in New Hamp-shire by 1997. Other areas present

unique problems. For example, a smallsalt marsh (<1 acre) was created onNew Castle Island at the southernentrance to Little Harbor as mitigationfor the Wentworth Marina. The marshfailed but was replanted by a new con-tractor following regrading and deploy-ment of wave barriers to reduce waveexposure. The marsh was replanted instages (from 1988 to 1992) and is grad-ually developing (Dr. D. Burdick, UNH,unpublished data).

Information on nineteen recent saltmarsh restoration projects is presented inTable 4.10. These data have been com-piled as part of a Gulf of Maine-wideproject (Cornelisen, 1998). The citedprojects were supported by many differ-ent agencies for a range of different pur-poses. The total estimated acreage ofsaltmarshes that have been targeted is433 acres, and the cost per acre rangedfrom $800 to $236,000. The high per acrecost of some of the compensatory proj-ects may be because of the requirementof the permit applicant to replace habitat

Area ProjectProject Title Funding Agency Town (acres) Cost/acre Type*

Sandy Point salt marsh NHOSP/CP Stratham/Greenland 5.0 rLittle River salt marsh North Hampton 156.0 rBass Beach salt marsh North Hampton 10.0 rAwcomin salt marsh NHOSP/CP;

USACE;USFWS Rye 35.0 $3,167 rLocke Road NH OSP/CP Rye 53.0 1,806 rHaul Road salt marsh Seabrook 0.5 c, rWentworth Marina New Castle 1.0 c, crMill Brook salt marsh restoration Stratham 10.0 rN.H. marine terminal mitigation NHPA Portsmouth 1.6 236,220 r, crSeabrook wastewater treatment facility Seabrook 0.6 c, rRye Harbor Rye 15.0 rRoute 101: Squamscott River bridge NHDOT Stratham 3.7 81,071 c, rWinnicut River salt marsh Greenland ? rFairhill saltmarsh restoration project Rye 12.2 rLanding Road salt marsh Hampton ? rStuart Farm NHOSP/CP Stratham 4.0 5,536Route 1-A NHOSP/CP Rye 40.0 1,229Drakeside Road NHOSP/CP Hampton 22.0 1,392Marsh Road NHOSP/CP Rye 50.0 800Total 419.6

* c= compensatory; r= restoration; cr= creation.

Recent saltmarsh restoration projects in New Hampshire (Cornelison, 1998). TABLE 4.10

function, often in close proximity to thesite of habitat loss (Cornelisen, 1998).High costs are a function of the removalof fill, planting, land acquisition andother expensive requirements. There is astark contrast in cost between low-costhabitat restoration projects, which arenot only lower cost projects but also canresult in much more acreage restored,and habitat creation projects.

4.4.3.4 Eelgrass Restoration

In addition to the mitigation activitiesdescribed below, eelgrass restorationefforts have been conducted on anexperimental scale at several sites in theGreat Bay Estuary (Carlson, 1997) andseveral more recent eelgrass restorationprojects have been funded by theUSEPA. One project is located in the Bel-lamy River and another is in Little Bay,where eelgrass beds, possibly killed bythe “wasting disease”, have not becomereestablished for over 10 years.

In Rye Harbor, another US EPA-fund-ed eelgrass restoration is designed to cre-ate eelgrass habitat and potentiallybenefit the ecological health of the har-bor. The eelgrass distribution in Rye Har-bor has been limited to a series of smallbeds in a perched intertidal tide pool.Reconfiguration of the storm-distributedrock and sediment material across a

broad area in the inner harbor will allowthe expansion of the tidepool eelgrasshabitat. To encourage this expansion,some transplanting will be done.

4.4.3.5 Port of New Hampshire Mitigation

When the N.H. Port Authority decided toexpand the State Port Facility by addinga new pier, containment structure, wharf,and two-lane connecting bridge, it wasclear that some estuarine habitat wouldbe destroyed or affected in the process.The U.S. Army Corps of Engineers andthe N.H. Wetlands Board issued a permitfor the $18 million construction, withState and Federal resource protectionagencies stipulating that the permitinclude provisions for mitigation of theprojected habitat loss (Short and Short,1997). Additionally, as an unusual provi-sion, the mitigation was required to meetspecific success criteria before actual portconstruction could begin. The NHPA Mit-igation Project cost $1.8 million. It is alarge and successful compensation forenvironmental impacts to the estuarywith sites located along the PiscataquaRiver and in Little Bay.

The multi-year mitigation projectcombined the efforts of the University ofNew Hampshire, the private consultingfirm of Dames and Moore, and a salt

198

Salt marsh restoration at Fairhill Marsh.

GBN

ERR

199

marsh restoration company based inMassachusetts called Great MeadowFarms. Eelgrass, salt marsh, and mud flathabitats were created during the three-year effort. The three-habitat mitigationwas meshed where possible, so that thehabitats could develop in proximity, asthey often do in nature. Finding sites forthe various mitigation was a major pre-liminary task. The mitigation work isnow complete and has entered a 15-yearmonitoring phase; this long-term moni-toring is another unique aspect of theproject.

More of each habitat was created orenhanced than was projected to be lostto construction of the new port facility.For eelgrass, the created:impacted ratiowas 1.4:1; for salt marsh the ratio was2:1; and for mud flats the ratio was 1:1.In part, these ratios were designed tocompensate for the gap in overall habi-tat values to the estuary as the newlycreated habitats established themselves.Transplanted salt marsh is particularlyslow to redevelop all of its functionsand values, and therefore had the high-est ratio.

Mitigation success criteria werebased largely upon “best estimate” andwere without strong scientific founda-tion. The mitigation project was held tosuccess criteria that included plant sur-vival and plant coverage. A NOAA-fund-ed research project based in part on theport mitigation determined what kinds ofcriteria are most effective in judging mit-igation success.

A total of 6.5 acres of eelgrass wastransplanted into the estuary, making thisthe largest eelgrass transplanting projectever done on the east coast. Several loca-tions were chosen along the PiscataquaRiver and in Little Bay, i.e., in quieterareas of these heavily travelled waters.Transplants put into intertidal sites large-ly failed, as eelgrass was scraped awayduring the following severe winter bylarge sheets of tidally-driven ice. Sub-tidal sites were largely successful andhave filled in to create new eelgrasshabitat. The mitigation efforts haveresulted in the development of new,

more effective methods for transplantingeelgrass (Davis and Short, 1997).

A unique aspect of the Port mitiga-tion project was its replacement not onlyof eelgrass habitat, but of potential habi-tat as well. The Port construction wasdue to impact areas where no eelgrassgrew, but that were very suitable for eel-grass growth and that likely sustainedeelgrass habitat in the past. Therefore,compensating for the loss of such poten-tial habitat was considered by the regu-latory agencies as they formulated thepermit for Port construction.

Creating new mudflat areasrequired finding previously-filledupland areas that could be excavatedand put back under water. Over 5 acresof mudflats were enhanced by increas-ing tidal flooding to a cove. A dam wasremoved and the channel deepened, sothat a previously rarely flooded area thatoften smelled bad is now flushed bytidal waters twice daily. New mudflatswere also created (1.4 acres) by exca-vating previously filled upland, resurfac-ing it with mudflat sediment, andgrading it to intertidal elevations (Griz-zle, 1997).

Kelp beds were created along theboulder borders of the Port mitigationterrace on the Piscataqua River. Propag-ules set on the boulders and grew rapid-ly over the two years since the terracewas installed, creating a new kelp foresthabitat.

Salt marsh was transplanted into twosites near the proposed Port expansionproject (Burdick, 1997). The salt marshsites were both chosen as being heavilydegraded estuarine shoreline in need ofenhancement and reconstruction. Ateach site, degraded estuarine shorelinewas reconfigured to conform to the tidalregimes required by salt marsh plants,which are very sensitive to submersiontimes and frequency. A total of 1.6 acresof salt marsh was transplanted (Table4.10), transforming a debris-strewnstretch of shoreline near an old railwaybed and a much-altered roadway andbridge abutment back into productiveestuarine habitat.

The review of technical informationon human uses and resource man-

agement in coastal New Hampshireshowed varying amounts of information

are available for the different areas ofconcern. The important observations ontrends and information gaps are pre-sented below.

200

� The population and density of the two coastal counties in New Hampshire haveexhibited steady increases over the past twenty years, and this trend is projectedto continue at a somewhat slower pace. The continuation of increases in popula-tion and density in New Hampshire’s two coastal counties is a concern becauseof the accompanying increases in development, use of coastal resources and pro-duction of pollutants, and the potential adverse impacts these factors can have onenvironmental quality.

� Commercial fishing is the coastal industry with the most significant economicactivity and employment. This industry is subject to destabilizing influences suchas world market prices, harvest pressure, government regulations, weather andabundance of wild stocks.

� Commercial lobstering has been the highest value fishery in New Hampshire.Landings have been relatively stable over the past decade, although extremeweather events have had adverse effects on the harvest in estuaries.

� There are some coastal communities that have high percentages of developedland and little more area available for development. In addition, much (40%) ofthe remaining developable land within 300 feet of tidal waters is permanentlyprotected.

� There is a wide variety of important vessel-related activities, including commercialfishing, shipping and recreational boating, the latter two of which may exhibit fur-ther increases in activity.

� Dredging activities are well coordinated and regulated and will continue to beimportant for maintenance of safe and accessible harbors.

� Aquaculture is beginning to become established in New Hampshire. The success-ful four-year operation of a land-based summer flounder facility is complementedby research and pilot projects on other finfish, shellfish and a variety of types ofaquaculture operations.

� Recreational activities such as boating, fishing, shellfishing and tourism are grow-ing in importance as economic activities in coastal New Hampshire.

� Recreational shellfishing is currently limited by water quality. Improvements inwater quality and management of shellfish resources that are anticipated as partof a bolstering of the State’s shellfish program will benefit all forms of recreationaland commercial uses and the environmental quality of coastal New Hampshire.

� Numerous recent and on-going studies have provided information to help plan-ners of future development to identify and prioritize ecologically important habi-tats for potential protection and conservation.

� Improvements in environmental quality and ecosystem integrity have been real-ized through efforts to restore habitats and species such as saltmarshes, eelgrassand anadromous fish. Other important habitats like shellfish beds are currentlythe subjects of research and will greatly benefit and provide enhanced estuarine-wide environmental quality from future significant restoration efforts.

4.5

SUMMARY OF FINDINGS

201

his report has been organizedinto four chapters, including anintroductory chapter and three

chapters covering the broad topics ofwater quality, living resources, andhuman uses and management ofresources. At the end of each chapterare summary lists of the significant find-ing within the chapter. No prioritizationwas made beyond separation of the list-ed, more significant findings from therest of the information in the chapters.

This chapter presents the findingsfrom the whole report in three tablesthat serve as a framework for prioritiz-ing identified problems. Issues are listedand identified as either being a problemor not in Table 5.1. Their causes,impacts and locations are identifiedalong with trends, solutions and agen-cies or organizations involved in

addressing the problems. The informa-tion in Table 5.1 is further distilled intoa list of priority documented problemsin Table 5.2. These problems are con-sidered to be the most significantbecause impacts have been document-ed and either human uses or environ-mental quality are directly affected.Thus Table 5.2 serves as a summary ofthe highest priority problems that couldbe addressed through NHEP activities.Table 5.3 is a list of potential problemsthat have a lower priority for immediateaction but could be significant in thefuture or under the right circumstances.The problems identified in these tablesare presented in the same order inwhich they appear in the first four chap-ters. Review of the appropriate chapterwill provide further details on any givenproblem.

5 SUMMARY OF FINDINGS

T

Storm drain stencilling.

J. PE

TERS

ON

202

Water/Sediment QualityMicrobial Pathogens/Fecal Bacteria

Nutrients

Trace metals: Chromium (Cr), Lead(Pb), Mercury (Hg)

Polyaromatic Hydrocarbons (PAHs)

PolychlorinatedBiphenyls (PCB)

Suspended Sediments

Toxic Algal Blooms

Living Resources:Shellfish

Oysters

Soft Shell Clams

Blue Mussels

Scallops

Lobsters

FinfishStriped bass

Winter flounder

Smelt

River herring

Shad

Silversides

Infaunal Benthos

Eelgrass

Saltmarshes

Macroalgae

Elevated concentrations

Loading to some rivers

Elevated concentrations insediments

Unknown

PCB residues elevated inlobster tomally

Unknown

Coastal

Low oyster population densities, reduced bed area

Decreasing density

Unknown

Unknown

Catch stable, some die off

No

Declining population,commercial and recreational catch

Unknown

Unknown

Decreasing returns

Unknown

No

Restricted tidal flow andchanges in vegetation

Loss of habitat

Cocheco R.Dry weather

Salmon Falls &Cocheco Rivers

Cr (Great Bay), Hg (Piscataqua R.)

Little Bay, Piscataqua R.

Seasonal occurrencesin tidal tribs to GreatBay & Piscataqua R.

Great Bay and tributary rivers

Little Bay, Rye Harbor

Unknown

Yes (duringwet weather)

No

Pb

Unknown

Yes

Unknown

Throughout theGulf of Maine

No

Unknown

Unknown

Unknown

Throughout theGulf of Maine

Unknown

Unknown

Unknown

Unknown

Yes

Unknown

Public health risk and shellfish closures

Intense blooms (Freshwater),isolated low dissolved oxygen (Salmon Falls River)

Unknown

Unknown

Lobster tomally consumption warning

Shellfish closure (mussels),potential public health risk

Loss of critical habitat, ecosystem functions, andeconomic activity

Loss of ecosystem function,and economic activity

Unknown

Unknown

Some dead from oil, more from freshwater

Loss of important commercialand recreational resource

Unknown

Unknown

Unknown

Unknown

Loss of salt marsh function

Unknown

Issue Problem Isolated Locations Throughout Impactswithin NH estuaries NH Estuaries

ENVIRONMENTAL ISSUES AND TRENDS

203

Yes

Yes

Yes

Yes

Yes

Yes

—

Yes

No

Yes(oil), No(Freshwater)

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

No

Decreasing

Unchanged

Decreasing

Down/episodic inc.

Decreasing

Decreasing 93-96

Unknown

Decreasing

Decreasing

Population increasing

Unknown

Stable

Increasing

Decreasing

No trend, highly variable

Some rivers up, other down

Decreasing returns

Insufficient data

Stable

Increasing since 1989

Increase in restored march acreage

Possibly increasing

Stormwater, Waste water treatment facili-ties bypasses and malfunctions, possiblefailing septic systems, and possibly illegaldirect discharges of septage

Waste water treatment facilities effluent,stormwater runoff

Historical sources, stormwater, municipaland industrial discharges, and atmosphericdeposition

Stormwater, vessels, oil spills

Historical discharges

Resuspension by wind, waves, tides and ice

Circulation patterns and toxic algae distri-bution in the Gulf of Maine

Sediment accumulation, cultch removal,disease, and poor spatfal

Sedimentation, predation,disease and pos-sibly harvest pressure

Current management and existing capturemethods

Good regional and local management

Overharvesting in Gulf of Maine

Unknown

Unknown

Possibly overharvest or predation

Unknown

Increased resource protection, recent lackof disease outbreaks, restoration efforts

Restoration of tidal flow and reduction infreshwater volume through stormwatermanagement

Possible local excess nutrients

Point source identification, stormwa-ter management, monitoring, localcode enforcement and innovativetreatment technologies

Reduce point source loading,stormwater management

Continued sediment and water qual-ity monitoring

Continued sediment and water qual-ity monitoring and spill prevention

Unknown

Continued sediment and water qual-ity monitoring

Continued phytoplankton and waterquality monitoring

Habitat restoration, disease monitor-ing, and resource management

Habitat restoration, resource assess-ment and management

None needed

Further research

Continued management

Continued management

Improve management and possiblestocks enhancement

Continue stocks assessment

Continue stocks assessment

Continue stocks assessment, andexamine stocking program

Consistent stocks assessment

Periodic monitoring

Continued protection, monitoring,restoration and mitigation

Continued restoration and stormwa-ter management

Research and monitoring

Documented Trend Suspected/Documented Causes Potential Solutions

204

Issue Problem Isolated Locations Throughout Impactswithin NH estuaries NH Estuaries

Phytoplankton

Freshwater Wetlands

Other Waterfowl

Eagles

Terns

Ospreys

Other IssuesShoreline Habitat

Upland Habitat

Conservation Lands

Impervious Surfaces

Shipping

Boating

Commercial fishingFinfish

Lobsters

Anadromous fish

Dredging

Late summer blooms during low flow periods

Loss of wetland acreage(some local gains)

No

No

Limited breeding in NH

No

Loss of shorelinehabitat acreage

Loss of upland habitatacreage

Acquisition of land andconservation easementsfor open space and habi-tat preservation

Increased area of impervi-ous surfaces

Potential for spills and dis-charges

Potential for spills, dis-charges and habitat dis-ruption

Declining stocks

Increasing Fishing effort

Unknown

Resuspension of potential-ly contaminated sedi-ments; loss of eelgrass

Salmon Falls River

Nearshore islands,coastal salt marshes

Great Bay

Piscataqua River

Cocheco RiverLittle Bay

No

Yes

Yes

Yes

No

No

Yes

Yes

Yes

Yes

No

Yes

Throughout theGulf of Maine

Yes

In all estuarinerivers

No

Low dissolved oxygen-Salmon Falls River

Loss of wetland habitat and function

Lower seabird diversity

Potential for decreased water quality, loss of habitatfunction

Potential for decreased water quality, loss of habitatfunction

Protection/loss of habitat

Water quality degradation,increased stormwater runoffvolume and velocity, loss ofhabitat

Oil spills and ballast watercontaminants

Illegal waste discharge, habi-tat destruction, other contam-inants (debris, oil&gas)

Tremendous economic impactand ecosystem alterations

Restoration of spawning habitat and improved accessto habitat

Re-introduction of historicalcontaminants to the estuarineenvironment

205

Documented Trend Suspected/Documented Causes Potential Solutions

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Unknown

Yes

Yes

Yes

Yes

Unchanged

Decreasing acreage overall

Increasing

Variable, possibly increas-ing seasonal population

Increasing

New nesting sites

Acreage lost is Increasing(rate unclear)

Increasing

Increasing

Increasing

No trend

Increasing/stable

Decreasing fish stocks

Stable

Increasing

Unknown

Phosphorus in waste water treatment planteffluent (low flow periods) and stormwaterrunoff

Acreage decreasing due to road construc-tion and residential and commercial devel-opment. Increased beaver population maycreate new wetland areas, often at expenseof surrounding upland properties

Habitat protection, restoration andresource management

Species preservation and habitat protection

Breeding colony being re-established

Establishment of nesting platforms

Residential and commercial development,increase in impervious surfaces generatingcontaminated runoff

Residential and commercial development,increase in impervious surfaces generatingcontaminated runoff

Growth, development and land use prac-tices reducing habitat values and functions

Residential and commercial development,road construction

Result from accidents and operator error.Ballast water discharge is a routine func-tion.

Lack of facilities, boater ignorance of conse-quences of their actions

Overharvesting and habitat destruction

Current management and existing capturemethods

Fish ladders, destruction of spawning habi-tat, and predation

Contaminant from historical and currentsources buried in sediments

Phosphorus removal and stormwatermanagement

Protection, mitigation

Continued protection, monitoring,resource management and habitatrestoration

Continued preservation, protectionand monitoring for environmentalrisk factors

Continued preservation, protectionand re-colonization efforts

Continued preservation, protectionand monitoring for environmentalrisk factors

Establishment of riparian buffers,local zoning, various land protectionand habitat restoration strategies,property owner education

Local zoning, various land protectionand habitat restoration strategies,property owner education

Continued land purchases and con-servation easements on local andregional levels

Local zoning, various land protectionand habitat restoration strategies,property owner education

Improved accident prevention, oilsspill response and potential treat-ment of ballast discharge

Education, pumpouts

Comprehensive management strate-gies, stocks enhancement, potentialfor aquaculture

Continued management

Continued management, researchand restoration activities

Research, continued dredge man-agement

206

Table 5.2 NHEP Priority Problems List: Documented Problems.

Problem Cause Impact Location Affected

CONTAMINANTS

Elevated concentrations Stormwater, CSO’s, septics, Shellfish bed closures Great Bay-of microbial pathogens WWTP’s (bypasses,infiltration), Potential public health risk Tidal rivers under all conditions

boats and illegal connections systemwide in wet weather Hampton- Tidal creeks

Tidal creeks under all conditionssystemwide in wet weather

Elevated sediment and Historical, municipal and No recent observations Localized hotspots: Cocheco,biota concentrations of industrial effluents, atmospheric Lamprey, Exeter rivers, PNStrace metals (Cr, Pb, Hg) deposition, Stormwater Systemwide means > regional means

Elevated concentration of Unknown/historical discharges? Consumption advisory Systemwide and regionalPCB in lobster tissue

Nutrient loading WWTP’s effluent Intense Plankton Blooms FW and isolated tidal portions of exacerbated by low f.w. flow depressed oxygen Cocheco and Salmon Falls rivers

LIVING RESOURCES

Declines in oyster Sedimentation, disease, Loss of valuable habitat Systemwidepopulations loss of cultch, poor recruitment Loss of ecosystem function

Loss of harvesting opportunities

Decreased clam density, Predation, harvest pressure, poor Loss of valuable habitat Systemwide and regionwideboom and bust fishery recruitment, mussel colonization, Loss of ecosystem function

disease (?) Loss of harvesting opportunities

Declining flounder Harvest pressure in Gulf of Maine Loss of harvesting opportunities Regionwidepopulations Predation(?) by bass, cormorants

Degraded saltmarshes Reduced tidal flow, development Change in vegetation localized areas (identified by NRCS)

Declines in alewife returns Unknown loss of important forage species Taylor River, Exeter River

207

NHEP Priority Problems List: Potential Problems. TABLE 5.3

Problem Contaminants Cause Potential Impact(s) Locations Potentially Affected

Nutrient enrichment WWTP’s, stormwater and NPS Algal blooms, marcroalgal Tidal: Exeter/Squamscott* Lamprey (?)(lawn fertilizer, septics) proliferation, low DO, Impoundments in freshwater rivers

eelgrass loss, decreased clarity

Toxic contamination Dredging Cocheco River redistribution of chromium & PAHs Cocheco & Piscataqua rivers

Oil spills Accidents Lethal and sublethal affects Piscataqua River and systemwide

Other Issues

Increase in impervious Development Change in quantity and timing of Systemwidesurfaces delivery of stormwater

Potential for increased contamination

Loss of riparian habitat Development Potential for increased Systemwidecontamination

Freshwater wetlands loss Development Potential for increased Systemwidecontamination

Loss of flood control function

Changes in circulation Dredging tidal flat erosion Hampton Harbor (Seabrook)patterns

209

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1998 Sanitary Survey for Lower Little Bay, Located in Newington, Dover, andDurham, New Hampshire (12/31/97). NH Department of Health and HumanServices. 29 pages of text, plus tables and figures.

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1994a Hampton Harbor Sanitary Survey Report. New Hampshire Department ofHealth and Human Services, Division of Public Health Services, Concord, NH.

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1992 Great Bay Sanitary Survey Report. DPHS 92-002. New Hampshire Division ofPublic Health Services, Concord, NH.

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subject to chemical analysis. Whereasmost samples had low to moderate con-centrations of metals, DDT and PCBs, ahigh PCB concentration (>2.9 ppm) wasfound in one sample from Hampton Har-bor (Figure 2.25), and a high concentra-tion (>125 ppm) of vanadium was foundin two samples from Rye Harbor. On theMaine side of Portsmouth Harbor, highconcentrations of copper (>342 ppm),lead (>285 ppm), mercury (>3.0 ppm)and zinc (>436 ppm) were measured innumerous samples from the PortsmouthNaval Shipyard.

The estuarine chemistry of tin in itsvarious inorganic and organic forms hasbeen extensively studied (Weber et al.,1995). The studies have largely occurredin the Great Bay Estuary, providing infor-mation on the concentrations anddynamics of tin species in coastal NewHampshire. The estuarine chemistry ofmercury has been the focus of morerecent studies by the same group (Pukand Weber, 1994; Weber et al., 1998).Ongoing and pending studies aredesigned to determine atmospheric dep-osition, extensive spatial determinationsof mercury concentrations in sediments,and elucidation of the biological cyclingof mercury species in saltmarsh sedi-ments in the Great Bay Estuary.

An assessment of fecal-borne micro-bial contaminants in sediments andwater around the Portsmouth Naval Ship-yard was made from September 1991 toJune 1993 (Jones, 1994). The purposewas to use fecal-borne bacteria as evi-dence for the presence of sewage-bornewaste materials, and to use such evi-dence to help establish the sources of thetoxic contaminants found around theShipyard. Measurements were made ofClostridium perfringens in water and insurface and subsurface sediments at 28sites in the vicinity of the shipyard and inYork Harbor from September 1991through June 1993. C. perfringens con-centrations were relatively low in watersamples near the shipyard and site 23 inYork Harbor had the consistently lowestlevels of all sites. The highest levels ofcontamination in surface sediments andsediment cores were generally near

Seavey Island, site 2 off New Castle andthe Rt. 95 bridge, while lower levels of C.perfringens were apparent at sites inchannels away from the Piscataqua Riverand in York Harbor. Sediment core pro-files showed highly contaminated layersat some sites. Comparison of C. perfrin-gens to lead and mercury concentrationsshowed similar trends in spatial distribu-tions. The relationship between tracemetal contaminants and the fecal-bornebacterial indicator suggests that somemetals in sediments around the shipyardare probably associated with sewageeffluent.

Besides microbial indicators of fecalcontamination, there are numerouschemicals that are useful indicators ofspecific sources of nonpoint source pol-lution. Studies on the Portsmouth NavalShipyard focused on a range of chemicalmarkers and indicator compounds forsewage, atmospheric deposition, petrole-um and runoff. Results suggested thatsewage is a major source of heavy met-als and toxic organic contaminants to thelower estuary, and other sources such asatmospheric deposition, urban runoffand petroleum spills also contribute con-taminants (Bowen and Pruell, 1994).

Overall, the estuarine sediments ofNew Hampshire are contaminated withsome trace metals and toxic organiccompounds at relatively high levels. Mostsignificant sources of contaminants arehistorical and similar or worse contami-nated conditions have existed for over 20years in some cases. The transport ofcontaminants with resuspended sedi-ments throughout the Great Bay Estuaryhas been documented. Of course, trans-port of floating oil during significantspills is a well-documented example ofcontaminant transport. The potential forcontamination even from remotesources, either naturally occurring or as aresult of dredging and oil spills, is anever-present threat. Prevention of furtherloading of contaminants where manage-ment is possible is thus an importantconcern. A coordinated monitoring pro-gram that includes periodic analysis ofsediments is needed to determine tem-poral trends for sediment contaminants.

235

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238

239

Population by Towns: US Census and NH OSP Projections. TABLE A-1

Area US Census OSP Est OSP Est OSP Est OSP EstTown (mi2) 1990 1993 1995 2005 2015

ROCKINGHAM COUNTY

Exeter 19.5 12481 12500 11995 11943 12017Greenland 13.6 2768 2863 2799 3085 3402Hampton 13.5 12278 12466 11970 12028 12641Hampton Fall 12.5 1503 1584 1424 1443 1529New Castle 2.0 840 835 825 849 874Newfields 7.3 888 964 800 736 749Newington 12.1 990 700 675 736 812Newmarket 13.8 7157 7308 7197 7952 8740North Hampto 13.8 3637 3733 3274 2858 2903Portsmouth 15.6 25925 22561 22766 24112 25033Rye 14.0 4612 4590 4048 3396 3371Seabrook 9.5 6503 6616 6547 7245 7959Stratham 15.2 4955 5224 5873 8066 9395Brentwood 16.8 2590 2677 2599 2858 3153Candia 30.2 3557 3589 3599 3962 4370Chester 26.0 2691 2812 2749 3113 3465Danville 11.7 2534 2766 2974 4047 4713Deerfield 51.9 3124 3194 3424 4273 4901East Kingsto 9.9 1352 1458 1349 1500 1654Epping 26.2 5162 5342 5548 6735 7616Fremont 17.2 2576 2703 2599 2858 3153Hampstead 14.4 6732 7056 7722 10216 11799Kensington 11.8 1631 1631 1599 1698 1842Kingston 20.8 5591 5651 5748 6594 7366Newton 9.9 3473 3527 3524 3849 4245Northwood 29.7 3124 3159 3299 3905 4370Nottingham 48.1 2939 3001 3199 3934 4432Raymond 29.3 8713 8925 9446 11999 13734Sandown 14.3 4060 4228 4773 6566 7647

STRAFFORD COUNTY

Dover 28.2 25042 25500 24324 24310 25767Durham 25.5 11818 11515 11416 11303 11937Madbury 14.0 1404 1456 1535 1853 2081Rollinsford 7.7 2645 2681 2594 2647 2828Barrington 49.1 6164 6406 6661 7954 8884Farmington 37.4 5739 5810 5888 6480 7077Lee 20.4 3729 3816 4374 5813 6679Middleton 18.6 1183 1181 1334 1715 1956Milton 34.7 3691 3758 4119 5122 5794NewDurham 45.0 1974 1973 2266 2947 3364Rochester 46.9 26630 26960 27078 29374 31948Somersworth 10.3 11249 11370 10812 10935 10990Strafford 52.0 2965 3083 3484 4639 5320

APPENDIX APopulation and Population Density of Rockingham and Strafford County Towns (NHOSP, 1997b)

TABLE A-2 Population Density By Towns: US Census and NH OSP Projections.

Area US Census OSP Est OSP Est OSP Est OSP EstTown (mi2) 1990 1993 1995 2005 2015

ROCKINGHAM

Exeter 19.50 640.05 641.0 615.13 612.46 616.26Greenland 13.60 203.53 210.5 205.81 226.84 250.15Hampton 13.50 909.48 923.4 886.67 890.96 936.37HamptonFalls 12.50 120.24 126.7 113.92 115.44 122.32NewCastle 2.00 420.00 417.5 412.50 424.50 437.00Newfields 7.30 121.64 132.1 109.59 100.82 102.60Newington 12.10 81.82 57.9 55.79 60.83 67.11Newmarket 13.B0 518.62 529.6 521.52 576.23 633.33NorthHampton 13.80 263.55 270.5 237.25 207.10 210.36Portsmouth 15.60 1661.86 1446.2 1459.36 1545.64 1604.68Rye 14.00 329.43 327.9 289.14 242.57 240.79Seabrook 9.50 684.53 696.4 689.16 762.63 837.79Stratham 15.20 325.99 343.7 386.38 530.66 618.09Brentwood 16.80 154.17 159.3 154.70 170.12 187.68Candia 30.20 117.78 118.8 119.17 131.19 144.70Chester 26.00 103.50 108.2 105.73 119.73 133.27Danville 11.70 216.58 236.4 254.19 345.90 402.82Deerfield 51.90 60.19 61.5 65.97 82.33 94.43EastKingston 9.90 136.57 147.3 136.26 151.52 167.07Epping 26.20 197.02 203.9 211.76 257.06 290.69Fremont 17.20 149.77 157.2 151.10 166.16 183.31Hampstead 14.40 467.50 490.0 536.25 709.44 819.38Kensington 11.80 138.22 138.2 135.51 143.90 156.10Kingston 20.80 268.80 271.7 276.35 317.02 354.13Newton 9.90 350.81 356.3 355.96 388.79 428.79Northwood 29.70 105.19 106.4 111.08 131.48 147.14Nottingham 48.10 61.10 62.4 66.51 81.79 92.14Raymond 29.30 297.37 304.6 322.39 409.52 468.74Salem 25.60 1005.70 1017.0 995.70 1018.13 1069.30Sandown 14.30 283.92 295.7 333.78 459.16 534.76

STRAFFORD

Dover 28.20 888.01 904.3 862.55 862.06 913.72Durham 25.50 463.45 451.6 447.69 443.25 468.12Madbury 14.00 100.29 104.0 109.64 132.36 148.64Rollinsford 7.70 343.51 348.2 336.88 343.77 367.27Barrington 49.10 125.54 130.5 135.66 162.00 180.94Farmington 37.40 153.45 155.3 157.43 173.26 189.22Lee 20.40 182.79 187.1 214.41 284.95 327.40Middleton 18.60 63.60 63.5 71.72 92.20 105.16Milton 34.70 106.37 108.3 118.70 147.61 166.97NewDurham 45.00 43.87 43.8 50.36 65.49 74.76Rochester 46.90 567.80 574.8 577.36 626.31 681.19Somersworth 10.30 1092.14 1103.9 1049.71 1061.65 1066.99Strafford 52.00 57.02 59.3 67.00 89.21 102.31

240

241

Drainage area and discharge for rivers entering the Great Bay Estuary. From Short (1992).

Drainage Areaa Mean Dischargeb Period Rivers (km2) cfs of Record

Lamprey 543 278 1934-77Squamscott 331 163c noneWinnicut 19 - noneOyster 78 19 1934-77Bellamy 85 25c noneCocheco 472 242c noneSalmon Falls 392 204 1968-78Piscataqua 414 210c none

Total 2334 1141

a drainage areas from Brown and Arellano (1979)b flow data from Normandeau Assoc., Inc. (1979)c Calculated from a regression of mean discharge = 0.5617 x area - 22.62 (R2=0.998)

based on dataa from the Lamprey, Oyster and Salmon Falls Rivers.

APPENDIX BDrainage Area and Discharge of Tributaries to the Great Bay Estuary

TABLE B-1

243

Definitions of Land Cover and Land Use

Land cover data were developed from LANDSAT Thematic Mapper imagery, 1988and 1990. For the purposes of the NEP nomination, some categories were collapsedfor simplicity.

Forested Land with tree cover, characterized by greater than 30 sq. feet/acre.

Wetland Based on National Wetlands Inventory Criteria, and indicating thepresence of hydric soils, hydrophytic vegetation, and evidence ofhydrology.

Urban Developed or built-up areas.

Agriculture Lands that are actively farmed, or pastureland.

Disturbed Land that has been altered to the extent that soil is exposed (e.g., gravel pits).

Cleared Other classes of cleared lands, including clear cuts, orchards, etc

Water Self explanatory.

Land use data was collected from a variety of sources including aerial photographyinterpretation, municipal tax records, and windshield surveys. Data sources werecolleected in late 1980s and early 1990s.

Forested/Open (default) Areas with no other uses present (default)

Single Family Residential Areas of detached single family residences

Multi Family Residential Areas of attached and detached multi-family residences, apartment complexes, ete.

Mobile Home Areas of delineated groupings of homes in subdivisions. Scattered mobile homes are included in Single Family Residential.

Commercial/Mixed Areas of retail and service establishments, as well asurban and non-urban areas where uses are too mixedto be mapped appropriately at the given scale. Alsorepresents educational, administrative, and religiousfacilities, as well as cemeteries.

Industrial Areas of manufacturing or non-retail eommereial facilities.

Recreational Public and private parks, recreational areas, play-grounds, ballfields, golf courses, sport facilities, and reserves.

Agriculture/Mining Crop and pasture lands, dairy, and livestock facilities,as well as areas with active resource extraction (e.g.,gravel pits).

Not Classified Areas with no data available.

APPENDIX CLand Cover and Land Use Classification and Areas for the Great Bay and Hampton Harbor Estuary Watersheds

(Complex Systems Research Center/UNH, 1995)

244

Watershed Land Cover for the Great Bay and Hampton/Seabrook estuaries (NH Portion)

Great Bay Estuary Hampton/Seabrook EstuaryCategory Acres % of Total Acres % of Total

Forested 296,070 66 10,094 40Wetland 44,703 10 5,392 21Urban 43,944 10 5,800 23Agriculture 28,418 6 2,039 8Disturbed 8,494 2 380 2Cleared 9,240 2 400 2Water 17,211 4 1,030 4

Watershed Land Use for the Great Bay and Hampton/Seabrook Estuaries (NH Portion)

Great Bay Estuary Hampton/Seabrook EstuaryCategory Acres % of Total Acres % of Total

Forested/Open (default) 271,080 57 19,341 77Single Family Residential 47,474 10 2,798 11Multi Family Residential 1,710 < 1 1,198 5Mobile Home 1,693 < 1 167 < 1Commercial/Mixed 11,345 2 1,130 4Industrial 3,118 < 1 282 1Recreational 12,216 3 128 < 1Agriculture/Mining 17,243 4 89 < 1Not Classified 96,958 20 — —

Note: Total acreage values for land use categories may not correlate well with those of landcover categories due to differences in catetgory definitions and data collection methods.Land cover data is derived from LANDSAT Thematic Mapper imagery, while land use data isderived primarily from aerial photo interpretation, municipal tax records, and windshieldsurveys of areas actively used for some purpose (for example, “agriculture” is defined andwas identified differently in the development of land use and land cover information;hence, total acreage values do not correlate well).

TABLE C-1

TABLE C-2

245

APPENDIX DAbundance and Value of New Hampshire Shellfish Resources

Abundance and Value of Shellfish Resources (N.H. Fish and Game)

CLAMS OYSTERS

Bushels of Value Bushels of Value @AREA Acres Adults @ $100/bu Acres Adults $60/bu

Hampton Harbor 242 19,400 $1,940,000 0 0 0Little Harbor Area 400 1,600 $160,000 0 0 0Great Bay Estuary

& Tributaries 2575 8,700 $870,000 52 51,931 $3,115,860

TOTAL 3217 29,700 $2,970,000 52 51,931 $3,115,860

TABLE D-1

TABLE D-2Estimated Great Bay Oyster Population Data

1981 1993 Open/Closed 1981 1993 Est. Bushels Est.Bushels

Bed Location Status Est. Acres Est. Acres per Bed per bed

Nannie Island Open 18.5 18.5 18,193 20,615Adams Point Open 2.0 5.1 1,794 8,358SW Great Bay Closed 9.8 no data 59,122 no dataOyster River Closed 7.4 6.0 12,062 10,038Bellamy River Closed 3.1 1.0 3,891 1,074Piscataqua River Closed 12.3 12.3 23,735 5,412

247

Species Common Name

MARINEAcipenseridae:

Acipenser oxyrhynhus Atlantic sturgeonAmmodytidae:

Ammodytes americanus American sand lanceBothidae:

Scopthalmus aquosus WindowpaneClupeidae:

Alosa aestivalis Blueback herringAlosa pseudoharengus River herring(Alewife)Alosa sapidissima American shadBrevoortia tyrannus Atlantic menhadenClupea harengus harengus Atlantic herring

Cottidae:Hemitripterus americanus Sea raven

Cyclopteridae:Cyclopterus lumpus Lumpfish

Gadidae:Gadus morhua Atlantic codPollachius virens PollockUrophycis chuss Red hakeUrophycis tenuis White hake

Labridae:Tautogolabrus adspersus Cunner

Osmeridae:Osmerus mordax Rainbow smelt

Pholidae:Pholis gunnellus Rock gunnel

Pomatomidae:Pomatomus saltatrix Bluefish

Rajidae:Raja erinacea Little skateRaja ocellata Winter skate

Salmonidae:Oncorhynchus kisutch Coho salmonOncorhynchus tshawytscha Chinook salmonSalmo salar Atlantic salmon

Serranidae:Centropristis striata Black sea bass

Species Common Name

ESTUARINEAnguillidae:

Anguilla rostrata American eelAtherinidae:

Menidia menidia Atlantic silversideCottidae:

Myoxocephalus aenaeus GrubbyCyprinodontidae:

Fundulus heteroclitus Common mummichogFundulus majalis Striped mummichog

Gadidae:Microgadus tomcod Atlantic tomcod

Gasterostidae:Apeltes quadracus 4-spine sticklebackGasterosteus aculeatus 3-spine sticklebackPungitius pungitius 9-spine stickleback

Percichthyidae:Morone americanus White perch

Petromyzontidae:Petromyzon marinus Sea lamprey

Pleuronectidae:Liopsetta putnami Smooth flounderPseudopleuronectes

americanus Winter flounderSyngnathidae:

Syngnathidae fuscus Northern pipefish

FRESHWATERCatastomidae:

Catastomus commersoni White suckerCentrarchidae:

Lepomis gibbosus PumpkinseedLepomis macrochirus BluegillMicropterus dolomieui Smallmouth bassMicropterus salmoides Largemouth bass

Cyprinidae:Notemigonus crysoleucas Golden shinerNotropis hudsonius Spottail shinerSemotilus corporalis Fallfish

Esocidae:Esox niger Chain pickerel

Ictaluridae:Ictalurus nebulosus Brown bullhead

Percidae:Perca flavescens Yellow perch

Salmonidae:Oncorhynchus mykiss Rainbow trout

Salvelinus fontinalis Brook trout

APPENDIX EFinfish and Intertidal and Subtidal Infaunal Invertebrate Species in the Great Bay Estuary

Species list of finfish collected from Great Bay Estuary, New Hampshire. Collections were made by fyke, haulseines, trawls and gill nets from July 1980 to October 1981 (Nelson 1981).

TABLE E-1

248

Phylum: RHYNCHOCOELANemertea spp. x x

Phylum: ANNELIDAClass: Polychaeta

Aglaophamus circinata x xAglaophamus neotenus xAmpharete spp. x xAricidea catherinae x xCapitella capitata x xChaetozone spp. x xClymenella torquata x xEteone heteropoda x xEteone longa xEteone spp. x xExogone hebes x xFabricia sabella x xHarmothoe spp. xHeteromastus filiformis x xHypaniola grayii xLumbrineris tenuis x xNephtys paradoxa xNephtys picta x xNephtys spp. xNereis diversicolor x xNereis zonata x xNereis spp. x xParaonis fulgens xPholoe minuta x xPhyllodoce maculata xPhyllodoce mucosa x xPhyllodoce spp. x xPolydora ligni xPolydora spp. xPraxillela gracilis xPrionospio steenstrupi x xPrionospio spp. xPygospio elegans x xScolelepis squamatus x xScolelepis spp. x xSpio spp. x xStreblospio benedicti x xTharyx acutus x

Class: Oligochaetaunidentified Oligochaeta spp. x x

Phylum: MOLLUSCAClass: Gastropoda

Haminoea solitaria x xHydrobia minuta x xHydrobia spp. xIlyanassa obsoleta x xLittorina littorea x xLunatia heros x xLunatia spp. xNassarius trivittatus xOdostomia spp. x x

Class: BivalviaCerastoderma pinnulatum xCrassostrea virginica x xEnsis directus xGemma gemma x xLysonia hyalina x xMacoma balthica x xModiolus modiolus x xMulinia lateralis x xMya arenaria x xMytilus edulis xNucula tenuis xNucula spp. xSolemya velum xTellina agilis x x

Phylum: ARTHROPODAClass: Crustacea

Ampelisca abdita/vadorum x xCaprella spp. x xCorophium spp. xCrangon septemspinosa x xCumacea spp. x xCyathura polita x xDiastylis polita xEdotea triloba x xGammarus mucronatus x xGammarus spp. xHarpinia spp. x xLeptognatha caeca xLeucon americanus x xLeucon nasicoides x xMicrodeutopus gryllotalpa x xMicrodeutopus spp. x xOxyurostylis smithi x xPhotis macrocoxa x xunidentified Copepoda spp. x xunidentified Ostracoda spp. x x

Phylum: HEMICHORDATAClass: Enteropneusta

Saccoglossus kowalevskii x

Intertidal and subtidal infaunal invertebrate species collected (retained on a 0.5 mm screen) inthe Great Bay Estuary, New Hampshire between June 1981 to May 1982 (Nelson 1982).

TABLE E-2

Intertidal Subtidal Intertidal Subtidal

249

Status and trends for water quality in coastal surface waters from 1988 to 1996: Overall quality and use support.

F= fully supporting all uses; P= partially supporting all uses; N= non-supporting all uses

FRESHWATER RIVERS AND STREAMS: MILES

Coastal Basin Piscataqua River Basin

F P N Total F P N Total

1988 21 2 5 28 111 41 31 1831990 24 4 0 28 83 45 55 1831992 59 0 15 74 950 21 30 10011994 72 2 0 74 957 22 22 10011996 74 0 0 74 990 6 5 1001

TIDAL WATERS: SQUARE MILES

Open Ocean Coastal Shoreline Estuaries

F P N Total F P N Total F P N Total

1988 NA NA 17.9 0.1 0 18 6.8 - 9.8 16.61990 NA NA 17.9 0.1 0 18 6.8 - 9.8 16.61992 53.8 0 0.2 54 18 0 0 18 9.5 — 18.7 28.21994 53.8 0 0.2 54 18 0 0 18 9.5 — 18.7 28.21996 54 0 0 54 18 0 0 18 10.5* 0.4 17.3 28.2

*Area reflects individual use support for shellfish consumption only.

APPENDIX FStatus and Trends for Overall Quality and Use Support for Water Quality in New Hampshire’s Coastal Surface Waters: 1988-1996.

(NHDES, 1996b, 1994, 1992, 1990, 1988)

TABLE F-1

250

TABLE F-2 Status and trends for water quality in coastal surface waters from 1988 to 1996: Overall quality and use support. (NHDES 1996b, 1994, 1992, 1990, 1988)

F= fully supporting all uses; P= partially supporting all uses; N= non-supporting all uses

INDIVIDUAL USE IMPAIRMENT (SQ MILES)SWIMMING*

Open Ocean Coastal Shoreline EstuariesF P N Total F P N Total F P N Total

1988 ALL — — ALL 17.9 0 0.1 18 ALL — — ALL1990 54 0 0 54 17.9 0 0.1 18 16.6 0 0 16.61992 53.8 0 0.2 54 18 0 0 18 16.6 0 0 16.61994 53.8 0 0.2 54 18 0 0 18 28.2 0 0 28.21996 54 0 0 54 18 0 0 18 28.2 0 0 28.2

AQUATIC LIFE SUPPORT

Open Ocean Coastal Shoreline EstuariesF P N Total F P N Total F P N Total

1988 no data no data no data1990 no toxicity data no toxicity data no toxicity data1992 54 0 0 54 18 0 0 18 28.2 0 0 28.21994 54 0 0 54 18 0 0 18 27.8 0.4 0 28.21996 54 0 0 54 18 0 0 18 4.4 23.8 0 28.2

*Some temporary closures of swimming areas in coastal waters have occurred as a result of heavy bather use.

251

Annual geometric means for fecal indicator bacteria at the three sites at low and high tides: 1988-97. TABLE G-1(Langan and Jones, 1997)

BOLD values for fecal coliforms designate values >14/100 ml, the standard for approved shellfish waters.

ADAMS POINT

Fecal Coliforms E. coli Enterococci C. perfringensYear High Low High Low High Low High Low

1988-89 29 15 5 4 2 11989-90 33 16 16 10 7 41990-91 23 17 15 13 5 61991-92 26 13 10 10 11 10 21 231992-93 12 11 11 9 2 2 9 121993-94 10 6 8 5 3 3 4 41994-95 7 6 4 3 3 2 4 61995-96 21 17 16 14 6 6 7 61996-97 14 13 11 10 4 4 5 7

Overall mean 17 12 10 8 4 4 6 8

SQUAMSCOTT RIVER

Fecal Coliforms E. coli Enterococci C. perfringensYear High Low High Low High Low High Low

1988-89 53 362 13 42 6 291989-90 44 234 24 137 12 601990-91 20 190 15 142 6 181991-92 24 148 19 81 14 48 44 731992-93 23 90 19 71 3 18 25 351993-94 12 61 10 54 5 27 10 221994-95 12 42 6 20 5 18 4 181995-96 51 128 28 104 13 56 16 151996-97 25 91 20 60 5 25 13 16

Overall mean 25 118 16 71 7 30 14 23

LAMPREY RIVER

Fecal Coliforms E.coli Enterococci C. perfringensYear High Low High Low High Low High Low

1991-92 114 214 101 191 5 12 11 171992-93 237 379 222 394 25 29 8 181993-94 100 225 90 178 22 33 4 121994-95 61 133 55 133 26 13 4 71995-96 268 588 195 497 86 169 12 171996-97 85 78 64 62 14 30 7 8

Overall mean 123 204 104 182 25 31 7 11

APPENDIX GFecal Coliform Data for Great Bay, Little Harbor, Rye Harbor and Hampton Harbor: 1985-1996.

252

TABLE G-2. Fecal coliform concentrations (per 100 ml) at sites in Little Harbor: 1988-1996 (NHDHHS).

FC/100 ML

Year T1 T5 T6 T7 T8 T9 T10 T13 T14 LH2 WC1

1988 7.1 109 8.5 28.2 156 77.3 24.51989 10.9 129 16.7 67.1 234 460 331990 16.4 84 31 57.8 128 196 14.51991 40.1 541 76.2 67.6 167 199 1901992 21.8 14.1 20.5 35.1 53.9 30.9 10.71993 6.9 4.2 18.6 14 7.3 18.9 11.71994 6 3.9 12.1 16.1 11.3 53 7.41995 2.6 3.3 7.5 49.8 5.4 7.7 8.4 2.6 10.1 2.8 56.41996 2.3 16.2 4.7 11.1 50.3 6.9 17.4 4.2 7.3 7 12.5

Overall average 8.3 28.7 14.1 23.5 29.3 38.2 64.4 13.7 8.6 5 26.6Last 30 average 4.3 5.5 9.4 23.5 17.3 13.3 23.1 13.7 8.6 5 26.6

NUMBER OF SAMPLES

Year T1 T5 T6 T7 T8 T9 T10 T13 T14 LH2 WC1

1988 11 10 11 9 10 9 111989 9 9 9 9 9 9 91990 4 4 4 4 4 4 21991 7 7 6 6 7 6 41992 6 5 6 6 6 7 31993 8 8 7 8 8 8 71994 8 7 7 8 7 8 61995 5 5 5 4 5 5 5 5 4 4 31996 8 8 9 7 2 4 3 10 10 7 3

Total samples 66 63 64 11 57 60 59 57 14 11 6

PERCENTAGE OF SAMPLES >43/100 ML

Year T1 T5 T6 T7 T8 T9 T10 T13 T14 LH2 WC1

1988 9 70 27 44 80 78 451989 22 89 22 67 89 89 441990 25 75 50 50 100 100 01991 71 86 83 67 86 100 1001992 17 20 17 50 50 29 331993 13 0 29 13 0 25 141994 13 14 14 38 29 50 01995 0 0 0 50 0 20 20 0 25 0 671996 0 38 0 0 50 0 0 10 20 14 33

Overall average 18 46 25 18 42 53 58 28 21 9 50Last 30 average 7 13 10 18 30 23 10 10 21 9 50

253

Fecal coliform concentrations (per 100 ml) at sites in Rye Harbor: 1985-1996 (NHDHHS). TABLE G-3

FECAL COLIFORMS/100 ML

Year RH1 RH2 RH3 RH4

1985 276 25 481986 51 6 4 61987 118 15 46 231988 53 13 3 71989 20 5 5 91990 18 12 6 91991 32 10 5 41992 7 5 6 101993 28 15 5 211994 17 13 5 201995 10 6 2 41996 3 6 2 4

Geometric mean 29 10 10 11Last 30 geo.mean 13.6 9.3 3.6 10.9

NUMBER OF SAMPLES

Year RH1 RH2 RH3 RH4

1985 2 2 21986 11 11 4 71987 17 16 6 151988 7 8 6 71989 8 8 6 81990 3 3 3 31991 6 6 6 61992 6 6 6 61993 9 9 6 91994 7 7 7 61995 4 4 4 41996 7 8 7 8

Total 87 88 63 79

FRACTION OF SAMPLES > 43/100 ML

Year RH1 RH2 RH3 RH4

1985 1 0.5 11986 0.55 0.18 0 0.141987 0.59 0.13 0.5 0.271988 0.57 0.25 0 0.141989 0.5 0.13 0 0.131990 0.33 0.33 0.33 0.331991 0.5 0.17 0.17 01992 0.17 0.17 0.17 0.171993 0.44 0.33 0 0.331994 0.14 0.14 0.14 0.331995 0.25 0 0 01996 0.14 0 0 0.13

Average 0.44 0.17 0.14 0.19Average 0.23 0.13 0.07 0.23

254

TABLE G-4 Fecal coliform concentrations at sites in Hampton Harbor: 1985-1996 (NHDHHS).

FECAL COLIFORMS/100 ML

Year HH 1A HH 2B HH 5B HH 5C HH 10 HH 11 HH 12 HH 17 HH 18 HH 19

1988 24 26 27 91989 10 14 17 51990 16 51 15 71991 38 18 28 211992 14 27 13 81993 16 11 15 10 12 8 11 13 11 91994 13 16 8 16 13 16 15 17 7 201995 9 9 8 7 6 5 6 8 3 71996 4 9 13 19 16 11 7 7 6 14

Overall average 15 13 13 10 11 10 10 12 6 12Last 30 average 12 11 11 10 9 8 8 8 4 11

NUMBER OF SAMPLES

Year HH 1A HH 2B HH 5B HH 5C HH 10 HH 11 HH 12 HH 17 HH 18 HH 19

1988 11 8 9 101989 7 1 1 81990 4 2 2 41991 6 5 5 61992 5 4 3 41993 37 44 35 15 45 15 36 45 16 191994 26 36 10 11 34 29 34 29 29 281995 9 25 25 24 17 17 17 17 25 171996 3 10 10 10 10 10 10 10 10 10Total samples 108 135 100 60 106 71 129 101 80 74

PERCENTAGE OF SAMPLES > 43FC/100 ML

Year HH 1A HH 2B HH 5B HH 5C HH 10 HH 11 HH 12 HH 17 HH 18 HH 19

1988 45 38 33 101989 14 0 0 131990 25 50 50 251991 67 40 60 501992 40 25 33 01993 35 20 29 13 16 0 22 20 25 161994 19 25 0 27 18 34 26 28 7 431995 11 4 8 4 0 12 0 12 4 121996 0 10 30 20 10 20 30 20 10 20Overall average 30 20 23 13 13 20 20 21 10 26Last 30 average 20 7 17 10 7 17 17 17 7 27

255

APPENDIX HTissue Concentrations of Toxic Contaminants in Bivalve Shellfish, Lobsters, Winter Flounder, and Marine Plants

SpeciesSite Ag As Cd Cr Cu Hg Ni Pb Zn

Zostera marina: leavesClark Cove 0.70 1.21 1.51 2.05 12.70 0.02 3.07 2.72 78.6Sullivan Pt. 0.83 1.52 1.62 1.74 11.20 0.02 1.73 1.88 85.7Dry docks 0.47 1.20 1.09 1.23 23.10 0.02 1.31 2.72 64.9Back Channel 0.63 1.17 1.03 1.50 13.80 0.02 1.41 2.25 66.4Jamaica Cove 0.73 1.54 1.05 2.89 17.00 0.02 1.79 3.78 71.1Piscataqua R. 0.70 1.01 1.22 0.92 15.00 0.01 1.58 1.27 67.0York Harbor 0.19 1.03 1.78 0.85 8.13 0.01 1.24 0.99 47.9Average 0.68 1.28 1.25 1.72 15.80 0.02 1.82 2.44 72.3

Zostera marina: rootsClark Cove 0.58 2.76 0.53 7.57 8.45 0.05 2.38 5.96 43.6Sullivan Pt. 0.76 6.62 0.61 7.55 12.00 0.04 3.43 10.90 72.9Dry docks 0.80 5.84 0.43 9.37 20.80 0.04 3.16 9.05 48.4Back Channel 0.61 4.90 0.49 12.40 29.40 0.05 3.60 19.70 67.4Jamaica Cove 0.64 3.00 0.58 11.60 18.60 0.06 3.13 11.10 61.9Piscataqua R. 0.54 3.76 0.56 6.56 12.00 0.03 2.84 8.48 46.3York Harbor 0.19 1.72 0.63 2.46 8.70 0.01 1.31 2.48 27.7Average 0.66 4.48 0.53 9.18 16.90 0.05 3.09 10.87 56.8

Spartina alternifloraClark Cove 0.26 1.20 0.04 1.97 1.91 0.02 0.80 1.12 36.1Sullivan Pt. 0.24 1.20 0.03 1.47 2.06 0.01 0.54 0.71 34.0Back Channel 0.24 1.20 0.08 2.76 2.54 0.02 0.86 1.73 40.9Jamaica Cove 0.14 1.20 0.08 1.44 3.23 0.01 0.68 0.63 18.9Piscataqua R. 0.17 1.20 0.04 1.89 1.84 0.01 0.41 0.73 32.9Spruce Creek 0.26 1.20 0.15 2.36 1.22 0.01 0.85 0.87 23.8York Harbor 0.12 1.20 0.10 2.82 1.27 0.01 1.50 1.27 23.6Average 0.22 1.20 0.07 1.98 2.13 0.01 0.69 0.97 31.1

Spartina patensClark Cove 0.10 1.20 0.03 0.87 1.84 0.02 0.52 0.59 20.6Sullivan Pt. 0.09 1.20 0.05 1.54 2.97 0.01 0.59 0.97 25.3Back Channel 0.15 1.20 0.11 2.50 3.56 0.01 1.11 2.11 47.7Piscataqua R. 0.22 1.20 0.16 3.52 3.70 0.02 1.75 4.08 22.1Spruce Creek 0.14 1.20 0.13 2.88 2.03 0.02 0.95 1.18 20.1York Harbor 0.11 1.20 0.14 1.06 1.89 0.02 0.59 0.54 11.1Average 0.14 1.20 0.10 2.26 2.82 0.02 0.98 1.79 27.7

Ascophyllum nodosumClark Cove 0.15 14.7 0.33 0.84 10.6 0.04 1.7 1.50Sullivan Pt. 0.65 2.1 0.78 0.63 31.4 0.03 3./ 0.60Storage yard 1.02 17.2 0.55 0.47 26.1 0.06 2.7 6.90 116.0Dry docks 0.33 15.2 0.37 0.76 10.1 0.03 1.1 1.03 63.9Jamaica Cove 0.32 26.8 0.70 0.97 6.30 0.04 1.70 53.1York Harbor 0.07 5.7 0.27 0.40 1.89 0.01 0.59 0.05 37.6Average 0.49 15.2 0.55 0.73 16.90 0.04 1.83 2.35 77.7

*From NCCOSC, 1997

Trace metal contaminant concentrations (dry weight) in marine plant tissues at sitesin New Hampshire and southern Maine.*

TABLE H-1

256 TABLE H-2 Tissue Contaminants in blue mussels at sites on or near the New Hampshire coast: 1982-1997.

Numbers in BOLD exceed the USFDA (1993) alert level for lead (11.5 µg/g dry weight). No other contaminant concentrations exceeded published USFDA alert levels oraction limits.

Site Location METALS (µg/g; dry weight) ORGANICS: (ng/g)Study*, year**, site # (wet weights converted assuming 15% DW)

NEW HAMPSHIRE Ag Al As Cd Cr Cu Fe Hg† Ni Pb Zn PCBs PAHs Chlr. pest.USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

Hampton Harbor, NH1993 GOMC (1997a) 0.05 94 2.1 1.6 6.4 274 0.46 1.4 2.4 123 10 71 4.21995 GOMC (1997c) 0.05 1.7 2.0 8.6 363 0.38 1.3 2.7 1431996 GOMC (1997d) 0.11 185 1.5 1.4 7.9 293 0.50 1.1 2.3 115 24 107 5.5

Rye Harbor, NH1994 GOMC (1997b) 0.10 125 1.4 1.5 6.5 280 0.61 1.4 2.1 90 5 71 3.51997 GOMC (1998) 0.06 180 1.5 2.1 7.0 313 0.64 1.7 2.3 117 12 69 12.0

Witch Creek, NHRye Isaza et al. (1989) 1.9 3.1 14.0 <0.2 2.5 6.7 100 260 14000

Isaza et al. (1989) 2.2 4.1 10.7 <0.2 <2.0 5.1 153 113 667

Little Harbor, NHNew Castle 1991 GOMC (1992) 0.90 2.7 9.0 45.5 330 0.50 4.2 5.2 270 16 <DL ND1992 GOMC (1994) 0.06 343 1.6 4.2 543 0.50 3.1 4.2 217 48 174 15.11995 GOMC (1997a) 0.05 2.2 2.7 8.8 510 0.69 1.7 6.5 155

Fort Point, NHNew Castle Isaza et al. (1989) 2.1 5.4 10.0 <0.2 <2.0 10.0 200.0 127 <6671991; #2 Johnston et al. (1994) 0.51 154 7.5 1.1 2.7 6.9 419 0.22 1.7 4.5 103

Goat I., NHPortsmouth Isaza et al. (1989) 2.3 7.3 9.3 <0.2 <2.0 8.7 153 267 4530

Shapleigh I., NHBack Channel 1991GOMC (1992) 0.08 1.8 8.0 30.5 513 0.40 3.4 5.0 130 28 <DL NDPortsmouth 1992 GOMC (1994) 0.08 370 2.2 4.5 750 0.67 2.7 5.6 167 74 378 17.91991; #11 Johnston et al. (1994) 0.15 273 7.3 1.7 4.1 7.8 680 0.27 1.6 9.2 119

Pierce’s I., NHPortsmouth Isaza et al. (1989) 2.7 7.3 8.0 <0.2 <2.0 <3.3 227 127 26001991; #14 Johnston et al. (1994) 0.13 302 10.7 1.5 3.8 5.8 579 0.72 1.7 5.7 89

257

Four Tree I., NHPortsmouth Isaza et al. (1989) 2.1 8.7 11.3 <0.2 <2.0 8.0 147 180 15300

Rt. 1 bridge, NH1991; #15 Johnston et al. (1994) 0.67 131 12.5 1.3 2.2 6.9 362 0.14 1.5 3.5 81

Atlantic Heights, NHPortsmouth Isaza et al. (1989) 2.1 4.7 10.0 <0.2 <2.0 8.7 180 160 3800

East Seafood Co., NHNewington Isaza et al. (1989) 2.7 4.8 15.3 <0.2 8.0 6.0 120 387 16701991; #24 Johnston et al. (1994) 2.20 581 9.3 1.9 6.2 9.1 1070 0.50 2.7 5.8 134

Piscataqua River, NHDover, 1991; #26Johnston et al. (1994) 2.80 508 11.1 4.3 8.6 11.4 1190 0.20 3.1 5.9 125

Piscataqua River (PSNH)/Little Bay, NH1991-93; #24-28NCCOSC (1997) 1.43 10.14 3.17 6.29 10.29 0.42 3.05 5.39 125 1646 145 46.9

Dover Point, NHHilton State ParkIsaza et al. (1989) 2.9 4.2 11.3 <0.2 4.7 5.8 100 393 1470Dover 1994 GOMC (1997b) 0.10 238 3.1 3.1 7.9 455 0.83 1.7 3.4 145 26 187 10.4July, 1996 GOMC (1997d) 66 658 2.2October, 1996 GOMC (1997d) 46 298 4.61997 GOMC (1998) 0.06 233 1.8 2.5 6.7 325 0.70 1.4 1.9 110 49 266 20.2

General Sullivan Br., NH1991; #27 Johnston et al. (1994) 1.20 193 8.0 2.5 5.1 8.2 489 0.46 2.6 5.8 140

Bellamy R., NHmouth; 1991; #28Johnston et al. (1994)1.90 388 13.5 2.0 4.4 8.5 638 0.29 1.9 2.8 142

Fox Point, NHNewington Isaza et al. (1989) 3.7 4.7 10.7 <0.2 6.7 5.6 87 293 733001996 GOMC (1997d) 78 1355 7.6

Nannie I., NHGreat Bay Isaza et al. (1989) 2.2 8.0 10.7 <0.2 3.9 8.7 87 613 12700

Site Location METALS (µg/g; dry weight) ORGANICS: (ng/g)Study*, year**, site # (wet weights converted assuming 15% DW)

NEW HAMPSHIRE Ag Al As Cd Cr Cu Fe Hg† Ni Pb Zn PCBs PAHs Chlr. pest.USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

258

Lamprey R., NHNewmarket Isaza et al. (1989) 3.3 57.0 16.0 <0.2 16.7 30.0 153 400 5200

NEW HAMPSHIRE &MAINEPortsmouth Hrbr, mouth-Rt.1 br. (1993) 0.19 10.31 1.64 4.25 8.25 0.44 2.09 6.09 98 745 72 26.91,2,11,14,16,170-73NCCOSC (1997)

MAINEMast Cove, ME1991; #25 Johnston et al. (1994) 1.20 305 6.5 2.0 3.8 7.0 655 0.35 2.0 3.9 120

Piscataqua R., MEI-95 to power line MEDEP (1993) 3.0 4.8 13.0 0.74 2.2 5.9 100

Rt. 1 bridge, ME1991; #16 Johnston et al. (1994) 0.10 294 5.7 1.7 3.8 7.1 679 0.30 2.3 6.6 117Badger I., MEKittery Isaza et al. (1989) 2.4 3.6 9.3 <0.2 <2.0 5.4 180 127 22701991; #17 Johnston et al. (1994) 0.85 316 5.1 1.1 3.3 6.4 626 0.28 2.0 5.2 93

Back Channel, MEE. bridge #32Gilfillan et al. (1985) 0.64 2.5 4.6 8.3 - 26.6 1051991; #18 Johnston et al. (1994) 0.06 223 8.0 1.9 3.5 6.1 648 0.39 1.4 10.9 981993; #18,167-169NCCOSC (1997) 0.23 10.14 2.08 4.09 12.04 0.44 1.93 13.14 113 849 80 34.2W. bridge; east endMEDEP (1993) - 2.4 3.8 8.9 0.58 12.0 150Back Channel, MEW. bridge; east end#5 Gilfillan et al. (1985) 0.51 2.5 5.5 7.8 7.2 90#31 Gilfillan et al. (1985) 0.70 2.4 4.2 8.4 5.9 80

Jamaica I., MEKittery Isaza et al. (1989) 1.9 4.5 8.0 <0.2 <2.0 9.3 127 147 44701991; #19 Johnston et al. (1994) 0.09 245 7.6 2.1 3.8 5.8 635 0.68 2.0 6.2 911993;#19,164-66NCCOSC (1997) 0.25 9.63 2.22 4.64 14.68 1.1 2.67 32.37 123 732 79 33.3

Clark Cove, ME1991; #3 Johnston et al. (1994) 0.08 203 13.2 1.9 3.0 5.5 434 0.44 1.6 5.2 921991; #4 Johnston et al. (1994) 0.61 348 10.5 0.1 4.0 7.6 617 0.22 1.4 10.3 1301991; #5 Johnston et al. (1994) 0.06 231 7.4 2.2 4.2 5.8 476 0.44 1.9 10.8 1091991; #6 Johnston et al. (1994) 1.2 237 8.8 1.9 3.7 8.4 573 0.16 1.8 9 132

Site Location METALS (µg/g; dry weight) ORGANICS: (ng/g)Study*, year**, site # (wet weights converted assuming 15% DW)

NEW HAMPSHIRE Ag Al As Cd Cr Cu Fe Hg† Ni Pb Zn PCBs PAHs Chlr. pest.USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

259

Clark Cove, ME (continued)1991; #7 Johnston et al. (1994) 0.85 294 6.3 1.6 3.4 7.5 627 0.24 2.4 10.7 1071991; #8 Johnston et al. (1994) 2.70 203 6.9 1.9 4.0 8.4 526 0.18 3.1 12.3 1191991; #161Johnston et al. (1994) 0.37 2.5 18.4 10.4 1110 0.45 9.0 7.5 97 61 6801991; #185Johnston et al. (1994) 0.06 189 1.7 6.0 7.8 596 0.32 3.0 5.0 1001993;3-#8,161-63NCCOSC (1997) 0.45 11.34 2.03 4.23 9.59 0.5 2.28 7.8 107 771 93 36.51993 GOMC (1997a) 0.28 187 2.4 3.3 7.5 535 0.74 2.6 5.4 126 70 154 11.11994 GOMC (1997b) 0.10 163 1.5 2.0 7.5 373 0.61 1.3 4.5 96 67 154 12.51995 GOMC (1997c) 0.12 1.8 3.3 9.9 535 0.56 1.7 6.1 1351996 GOMC (1997d) 0.10 335 1.7 2.9 8.2 518 0.86 1.4 5.1 113 38 203 7.31997 GOMC (1998) 0.06 428 1.6 3.0 7.0 610 0.66 1.9 5.1 125 37 147 15.3

Clark I., MEKittery Isaza et al. (1989) 2.3 4.0 7.3 <0.2 <2.0 5.8 167 120 1600

Sullivan Pt., MESeavey I. #15Gilfillan et al. (1985) 0.50 3.6 5.7 7.4 - 8.1 901991; #9 Johnston et al. (1994) 0.08 154 6.0 1.8 3.2 5.7 377 0.34 1.5 7.2 1051993;#9,159,160NCCOSC (1997) 0.19 8.76 1.97 3.23 7.55 0.32 1.63 7.27 98 949 70 51.8

Henderson Pt., MESeavey I. #16Gilfillan et al. (1985) 0.60 2.9 6.0 8.2 - 5.4 811991; #10AJohnston et al. (1994) 0.04 76.9 5.1 1.9 2.3 6.2 209 0.13 1.5 26 1221993;10.5,156-158NCCOSC (1997) 0.21 6.75 1.86 3.81 15.66 0.3 2.44 75.96 111 725 125 35.9

Dry Dock/Seavey I., ME1991; #10 Johnston et al. (1994) 0.03 522 8.4 2.0 3.4 8.1 497 0.97 1.4 13.5 2221991; #12AJohnston et al. (1994) 0.15 330 6.9 2.5 3.8 9.0 825 0.41 2.2 9.6 1211991; #12 Johnston et al. (1994) 0.07 280 6.5 3.1 3.5 32.3 536 0.45 2.3 11.0 1051993; #10,12,17,NCCOSC (1997) 0.34 8.3 2.22 3.94 12.14 0.48 2.2 8.08 107 2540 84 27.1

151-155

Spruce Creek, MEupstream #26AGilfillan et al. (1985) 0.68 2.5 5.3 7.1 - 6.9 851991; #21 Johnston et al. (1994) 0.12 650 7.9 9.3 5.8 7.4 1300 2.1 6.4 125

MEDEP (1993) - 1.5 2.6 7.9 0.39 5.9 110

Spruce Creek, MEdownstream #20Johnston et al. (1994) 2.60 452 7.6 1.5 4.4 7.9 820 0.26 2.1 6.7 1341993; #20, 21 NCCOSC (1997) 1.36 7.75 5.4 5.1 7.65 0.26 2.1 6.55 130 821 103 34.6

Site Location METALS (µg/g; dry weight) ORGANICS: (ng/g)Study*, year**, site # (wet weights converted assuming 15% DW)

MAINE Ag Al As Cd Cr Cu Fe Hg† Ni Pb Zn PCBs PAHs Chlr. pest.USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

260

Pepperill Cove, MEKittery MEDEP (1993) 2.5 3.9 9.1 0.57 2.3 11.0 1101991; #1 Johnston et al. (1994) 0.17 317 8.4 1.4 3.8 5.8 600 0.43 1.7 6.2 96

Fort Foster, MEwest end; #30CGilfillan et al. (1985) 0.55 2.2 7.3 7.4 4.2 80

Fort Foster, MEeast end; #RPGilfillan et al. (1985) 0.62 2.6 5.6 6.8 3.7 89

Horn I., MEKittery #HIGilfillan et al. (1985) 0.58 2.6 3.5 6.8 3.5 88

White I., MEKittery #WIGilfillan et al. (1985) 0.65 2.6 3.3 6.1 4.0 85

Wood I., MEKittery #WOODGilfillan et al. (1985) 0.66 3.5 5.4 8.3 5.8 93

Brave Boat Harbor, MEYork & Kittery MEDEP (1993)1993; #175Johnston et al. (1994) 0.87 ND 3.5 8.1 840 0.21 1.8 111 3 168 ND1993; #186Johnston et al. (1994) 0.18 94 1.5 4.3 5.7 725 0.18 2.8 1.7 67 ND ND ND1993 GOMC (1997a) 0.20 177 2.8 3.1 7.1 469 0.71 3.0 3.5 118 ND ND ND1996 GOMC (1997d) 0.30 290 1.7 1.5 6.6 353 0.42 1.5 1.8 110 ND ND 0.6

York Harbor, MEupstream #22Johnston et al. (1994) 0.07 197 3.9 1.4 2.0 6.0 341 0.11 1.0 1.9 891991; #23 Johnston et al. (1994) 0.11 176 5.7 1.4 1.9 6.5 385 0.31 1.2 1.9 831993; 22,23,123NCCOSC (1997) 0.17 7.31 1.49 1.87 7.5 0.23 1.08 2.06 83 481 39 19.8

Saco River, MEriver mouth MEDEP (1993)1994 GOMC (1997b) 0.10 103 1.6 1.6 6.3 288 0.56 1.1 2.5 86 13 49 5.6

MASSACHUSETTSMerrimack River, MAmouth 1993 GOMC (1997a) 0.14 49 2.8 2.6 6.5 393 1.08 1.5 4.8 113 44 162 6.8

*Refer to bibliography for study citations. PNS samples include all results from 1991 (Johnston et al., 1994) and 1993 (NCCOSC, 1997).**Dates for GOMC and PNS studies are sample dates. Sample dates for Gilfillan et al. are 1982 & 1983; MEDEP are 1988-1992; Isaza are 1987.†Some GOMC Hg results are suspiciously high.

Site Location METALS (µg/g; dry weight) ORGANICS: (ng/g)Study*, year**, site # (wet weights converted assuming 15% DW)

MAINE Ag Al As Cd Cr Cu Fe Hg† Ni Pb Zn PCBs PAHsChlr. pest.USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

261

TABLE H-3 Trace metal and toxic organic contaminant concentrations (dry weight) in oysters, soft-shelled clams and ribbed mussels at sites in New Hampshire and southern Maine.

Species Information source Ag As Cd Cr Cu Hg Ni Pb Zn totPAH totPCB totDDxSite, Date µg/g µg/g µg/g µg/g µg/g µg/g µg/g µg/g µg/g ng/g ng/g ng/g

Crassostrea virginicaNannie I, 1986 Nelson, 1986 3.5 4.9Piscataqua River Nelson, 1986 4.5 4.6Bellamy River Nelson, 1986 2.25 3.7Oyster River Nelson, 1986 2.7 3.8Nannie I. 1992 Langan & Jones, 1995 7.4 2 1.1 1 564Nannie I. 1994 Langan & Jones, 1995 7.2 1 0.68 1 442Fabian Pt 1992 Langan & Jones, 1995 8 3.9 1.3 2 490Fabian Pt 1994 Langan & Jones, 1995 7.6 2 1 2 461Pierce Pt. 1992 Langan & Jones, 1995 6.4 2 0.95 1 648Pierce Pt. 1994 Langan & Jones, 1995 4.1 1.5 0.54 1 285MacIntyre Bk 1991 Weston, 1992* 5.58 114 0.7 2.3 3767Adams Point 1991 Weston, 1992 4.33 171 0.8 5.16 5283Fox Point, 1996 Chase et al., 1997 1145 116 39Upper GBE, 1991-93 NCCOSC 1997 12.5 10.1 4.41 2.94 266 0.28 3.27 1.75 6004 985 227 110Upper Pisc. R., 1991 Johnston et al. 1994 17.6 4.3 6.8 2.6 257 0.2 2.7 0.85 5080 203 88.4Boston Harbor, 1991 Johnston et al. 1994 19.9 8.8 3.7 3.8 208 0.17 4.1 1.3 5830 214 159Adams Point, 1991 Johnston et al. 1994 12.3 5.8 3.5 3.1 187 0.07 2.7 1.1 4620 189 126Nannie I., 1991 Johnston et al. 1994 22.6 5 4.3 2.2 301 0.19 3 0.61 7100 246 109Average 16.98 6.51 4.5 2.7 214.9 0.6 3.154 2.2 5383.4 627.5 199.2 105.2

Mya arenariaNannie I., 1987 Isaza et al., 1989 0.3 6.0 <0.2 5.6 22000 207Pierce Point Isaza et al., 1989 1.4 26.7 <0.2 36 <0.67 227Fox Point Isaza et al., 1989 1.3 9.3 <0.2 10 31333 127Bellamy River Isaza et al., 1989 0.8 11.3 0.29 12 <0.67 247Hilton State Park Isaza et al., 1989 1.0 8.7 <0.2 13.3 38000 113Three Rivers Point Isaza et al., 1989 1.3 14.7 <0.2 12 3400 127Witch Creek Isaza et al., 1989 0.3 8.0 <0.2 8.7 35333 <66.7Seabrook Isaza et al., 1989 1.4 4.3 15.3 0.3 9.3 8 80 80MacIntyre Bk 1991 Weston, 1992 20.6 11.3 0.4 12.5 59.4Average 20.6 1.0 11.1 13.3 04. 9.3 13.1 69.7 26013.3 161.0

Geukensia demissusMacIntyre Bk 1991 Weston, 1992 5.87 6.7 0.7 2.4 34.7Adams Point 1991 Weston, 1992 4.87 7.3 0.6 2 43.3Average 5.37 7 0.6 2.2 39

USFDA Action Levels for Shellfish 25 87 6.7 533 11.5 13000 33000

* Weston (1992), Nelson (1992) and Isaza et al. (1989) results based on wet weight. Data shown assume 12% (oysters),15% (mussels) and 16% (clams) dry weight.

262 TABLE H-4. Trace metal and toxic organic contaminant concentrations (dry weight) in lobsters (Homarus americanus) and winter flounder (Pleuronectes americanus) at sites inNew Hampshire, Maine and off-shore areas.

Tissue type Information source Ag As Cd Cr Cu Hg/ Ni Pb Zn PAHs PCBs DDT andSite methylHg total total metabolites

LOBSTERS µg/g µg/g µg/g µg/g µg/g µg/g µg/g µg/g µg/g ng/g ng/g ng/g

Juveniles-tail + clawClark Cove NCCOSC (1997) 0.50 5.1 0.01 0.12 18.1 0.88 0.15 0.05 84 135 18.0 3.16Sullivan Pt. NCCOSC (1997) 0.74 4.83 0.01 0.21 30.5 0.96/0.15 0.19 0.06 119 168 11.3 2.67Dry docks NCCOSC (1997) 0.46 4.35 0.01 0.21 2.39/4.61 0.22 0.05 117 485 63.5 11.40Jamaica Cove NCCOSC (1997) 0.60 6.72 0.03 0.24 25.3 0.73 0.29 0.06 123 161 11.8 2.01Isles of Shoals NCCOSC (1997) 0.60 10.54 0.01 0.25 23.6 0.39 0.22 0.05 99 52 15.0 3.57

Juveniles-hepatopancreasClark Cove NCCOSC (1997) 1.07 12.17 7.06 0.29 150.0 0.21/0.13 0.58 0.08 79 2685 1017.0 498.00Sullivan Pt. NCCOSC (1997) 1.44 12.33 8.05 0.25 151.0 0.22/0.08 1.00 0.07 102 3596 848.0 398.00Dry docks NCCOSC (1997) 2.72 9.67 5.72 0.48 0.31 0.87 0.10 119 8371 1429.0 554.00Jamaica Cove NCCOSC (1997) 1.27 14.65 6.71 0.40 148.0 0.24 0.91 0.12 90 4007 877.0 326.00Isles of Shoals NCCOSC (1997) 0.54 12.77 11.68 0.34 83.6 0.17 1.81 0.19 71 225 814.0 426.00

Sublegal adults-tail + clawPortsmouth Hbr. NCCOSC (1997) 0.54 10.07 0 0.24 26.2 1.01 0.18 0.04 115 72 19.0 3.36Isles of Shoals NCCOSC (1997) 0.70 13.73 0.01 0.36 23.3 0.51 0.31 0.06 115 48 33.0 7.08

Sublegal adults-hepatopancreasPortsmouth Hbr. NCCOSC (1997) 3.01 12.09 5.16 0.36 112.0 0.22/0.07 0.52 0.17 59 3495 1130.0 553.00Isles of Shoals NCCOSC (1997) 2.26 19.64 15.37 0.38 257.0 0.18 1.32 0.09 74 675 1587.0 779.00

Adults-tail + clawPortsmouth Hbr. NCCOSC (1997) 0.25 7.60 0.01 0.26 15.3 0.51/0.28 0.19 0.05 100 111 18.9 4.76Isles of Shoals NCCOSC (1997) 0.50 19.09 0.01 0.18 22.2 0.74/0.97 0.18 0.08 104 209 17.2 3.28Brave Boat Hrbr Sowles et al. (1996) 0.80 24.00 0.26 1.02 50.0 0.72 0.70 140 82ME reference sites Sowles et al. (1996) 1.10 21.00 0.18 0.59 42.0 0.43 1.30 178 135

Adults-hepatopancreasPortsmouth Hbr. Johnston et al. (1994) 1.02 13.06 13.48 0.41 542.0 0.35/0.12 0.56 0.38 66 1504 1362.0 812.00Isles of Shoals Johnston et al. (1994) 0.46 17.52 12.89 0.22 173.0 0.2/0.11 2.00 0.32 70 332 1093.0 508.00Brave Boat Hrbr Sowles et al. (1996) 5.10 24.00 21.00 0.37 380.0 0.29 0.53 62ME reference sites Sowles et al. (1996) 3.85 19.00 15.00 0.33 195.0 0.20 0.70 48

263

Mixed adult/juvenile-tail + clawPortsmouth Hbr. Johnston et al. (1994) 0.68 12.93 0.04 0.74 25.7 1.3 0.53 0.41 81 2267 32.8 7.3York Harbor Johnston et al. (1994) 27.8 7.34

Mixed adult/juvenile-hepatopancreasPortsmouth Hbr. NCCOSC (1997) 1.44 19.73 13.18 0.58 256 0.22 1.28 0.34 74.5 4111 1466 667York Harbor NCCOSC (1997) 1181 791

Adults-musclePierces I. Isaza et al., 1989 <0.23 0.92- 37- 0.14- <1.4 <2.3 92- <.5- <0.05-

(assume 21.7% dry weight) 1.38 69 0.51 147 12900 66400Adults-viscera Pierces I. Isaza et al., 1989 6.5- 1.4- 129- <0.14- 1.4- <2.3 78- 21200- 1705-

(assume 21.7% dry weight) 9.2 1.6 332 0.46 2.8 111 87600 50700Adults (cooked)-meatLittle Bay Schwalbe and Juchatz (1991) <300 <20

Adults (cooked)-tomalley Little Bay Schwalbe and Juchatz (1991) 490 70

US FDA Action Levels for Shellfish 25 87 6.7 533 12 13000 33000

WINTER FLOUNDER

FleshPortsmouth Hbr. NCCOSC (1997) 0.008 5.75 0.010 0.23 0.27 0.21/0.25 0.18 0.06 16.4 17.2 51.5 6.61Portsmouth Hbr. Johnston et al. (1994) 0.034 6.41 0.040 0.73 3.58 0.10 0.65 0.37 38.4 518 87.4 24.8Gulf of Maine NCCOSC (1997) 0.004 31.1 0.010 0.28 0.28 0.4/0.23 0.30 0.08 12.3 18.9 67.6 11Tork Harbor Johnston et al. (1994) 26.3 5.38

LiverPortsmouth Hbr. NCCOSC (1997) 0.464 3.37 0.16 0.27 15.3 0.13/0.05 0.58 0.28 89.4 59.6 938 163Portsmouth Hbr. Johnston et al. (1994) 0.66 2.10 0.09 0.40 22.0 0.53 0.24 114 531 838 192Gulf of Maine NCCOSC (1997) 7.63 25.6 3.64 0.40 84.2 0.3/0.12 3.63 2.82 131 54.8 787 180York Harbor Johnston et al. (1994) 658 175

Tissue type Information source Ag As Cd Cr Cu Hg/ Ni Pb Zn PAHs PCBs DDT andSite methylHg total total metabolites

265

HoloplanktonAcartia hudsonicaAcartia spp. copepoditesCalanus finmarchicus copepoditesCopepod nauplii, undifferentiatedEurytemora spp. copepoditesEvadne spp.Microsetella norvegicaOithona spp. naupliiOithona spp. copepoditesPodon spp.Pseudocalanus spp. copepoditesPseudocalanus/Calanus naupliiRotiferaTintinnida

MeroplanktonAnomia spp. veligersBivalve umbone veligers,

undifferentiatedBivalve straight-hinge veligersCirripedia cypridsCirripedia naupliiGastropoda veligersHiatella spp. veligersModiolus modiolus veligersMytilus edulis veligersPolychaete larvaePolychaete eggs

TychoplanktonForaminiferaHarpacticoida

APPENDIX IZooplankton Species in the Great Bay Estuary

Zooplankton species collected from the Great Bay Estuary, New Hampshire during 1979 (NAI 1980). TABLE I-1

267

CHLOROPHYTAAcrochaete repens x** ABlidingia minima x x x x x x x x x x AABryopsis plumosa x x x x x ACapsosiphon fulvescens x x x x x AChaetomorpha aerea x PChaetomorpha brachygona x x x AChaetomorpha linum x x x x x PChaetomorpha melagonium x x PChaetomorpha picquotiana x x x PCladophora albida x x AACladophora pygmaea x x x PCladophora sericea x x x x x x x x x x AA/PPCodiolum gregarium x x** ACodiolum pusillum x** AEnteromorpha clathrata x x x x x x x x AEnteromorpha compressa x x x x x AAEnteromorpha flexuosa ssp. flexuosa x AEnteromorpha flexuosa ssp. paradoxa x x x x x x x x AEnteromorpha intestinalis x x x x x x x x x AAEnteromorpha linza x x x x x x AAEnteromorpha prolifera x x x x x x x x x x AAEnteromorpha torta x x AEntocladia viridis x x AAKornmannia leptoderma x x AMicrospora pachyderma x** x x x AMonostroma grevillei x x x AMonostroma pulchrum x x AMougeotia sp. x AOedogonium sp. x APercursaria percursa x x AAPrasiola stipitata x AAPseudendoclonium submarium x AARhizoclonium riparium x x x x x x x x x x AARhizoclonium tortuosum x x x x x AASpirogyra sp. x ASpongomorpha arcta x x ASpongomorpha spinescens x x AStigeoclonium sp. x x AUlothrix flacca x x x x x x x x x AUlothrix speciosa x x AUlva lactuca x x x x x x x x x A/PPUlvaria obscura x x x x x x AUlvaria oxysperma x x x x x x x x x AUrospora penicilliformis x x x AUrospora wormskioldii x x A

Total Chlorophyta Taxa 35 37 25 14 12 11 20 11 14 4

* = Longevity designations (A = annual, AA = aseasonal annual, P = perennial, PP = pseudoperennial) ** = Only found in culture

APPENDIX JSpecies of Seaweeds and Plants Occurring in New Hampshire Salt Marshes

Pisc

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Summary of seaweed species composition from ten Great Bay estuarine areas (modified fromMathieson and Penniman 1991).

TABLE J-1

268

PHAEOPHYTAAgarum cribrosum x PAscophyllum nodosum x x x x x x x x x PAscophyllum nodosum

ecad scorpioides x x x x x PChorda filum x x AChorda tomentosa x x AChordaria flagelliformis x x ADelamarea attenuata x ADesmarestia aculeata x PDesmarestia viridis x ADesmotrichum undulatum x ADictyosiphon foeniculaceus x AEctocarpus fasciculatus x AEctocarpus siliculosus x x x x x x AElachista fucicola x x x PFucus distichus ssp. distichus x PFucus distichus ssp. edentatus x PFucus distichus ssp. evanescens x x x x PFucus spiralis x x x PFucus vesiculosus x PFucus vesiculosus var. spiralis x x x x x x x x x PGiffordia granulosa x x AGiffordia sandriana x x AIsthmoplea sphaerophora x x** ALaminaria digitata x x PLaminaria longicruris x x PLaminaria saccharina x x x PMyrionema corunnae x AMyrionema strangulans x x x APetalonia fascia x x x x x APetalonia zosterifolia x APetroderma maculiforme x x x PPilayella littoralis x x x x x x x APseudolithoderma extensum x x x PPunctaria latifolia x x ARalfsia bornetii x x x P(?)Ralfsia clavata x x x P(?)Ralfsia fungiformis x PRalfsia verrucosa x x x PScytosiphon lomentaria

var. complanatus x AScytosiphon lomentaria

var. lomentaria x x x x ASorocarpus micromorus x ASphacelaria cirrosa x x x PSpongonema tomentosum x P(?)Stictyosiphon griffithsianus x x AUlonema rhizophorum x x A

Total Phaeophyta Taxa 38 35 18 7 4 3 8 2 2 0

Pisc

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Summary of seaweed species composition (continued)TABLE J-1

269

RHODOPHYTAAhnfeltia plicata x x x PAntithamnion cruciatum x x x x AAntithamnionella floccosa x x x AAAudouinella membranacea x x x P(?)Audouinella purpurea x x PAudouinella secundata x x x x AAAudouinella violacea x x x ABangia atropurpurea x x x ABonnemaisonia hamifera x x x PCallithamnion byssoides x x ACallithamnion hookeri x x ACallithamnion tetragonum x x x x x x x x PCallocolax neglectus x P(?)Callophyllis cristata x PCeramium deslongchampii

var. hooperi x x P(?)Ceramium elegans x ACeramium rubrum x x x x x x x x PCeramium strictum x x x x x x x x x AChondria baileyana x x x x x x AChondrus crispus x x x x x x x PChoreocolax polysiphoniae x PClathromorphum circumscriptum x x x PCorallina officinalis x PCruoriopsis ensis x P(?)Cystoclonium purpureum

var. cirrhosum x x x PCystoclonium purpureum

forma stellatum x PDasya baillouviana x x x x x x x x x ADermatolithon pustulatum x x x PDumontia contorta x x x AErythrotrichia carnea x x x x AFimbrifolium dichotomum x PFosliella lejolisii x x x PGloiosiphonia capillaris x AGoniotrichum alsidii x x x AGracilaria tikvahiae x x x x x x x PGymnogongrus crenulatus x x x x PHildenbrandia rubra x x x x x PLeptophytum laeve x PLithophyllum corallinae x PLithothamniom glaciale x PLomentaria baileyana x x x x ALomentaria clavellosa x x x P(?)Lomentaria orcadensis x x PMastocarpus stellatus x x PMembranoptera alata x PPalmaria palmata x x x x PPetrocelis cruenta x x PPeyssonnelia rosenvingii x x x PPhycodrys rubens x x P

Pisc

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Summary of seaweed species composition (continued) TABLE J-1

270

Phyllophora pseudoceranoides x x x PPhyllophora truncata x x x PPhymatolithon laevigatum x x PPhymatolithon lenormandii x x PPolyides rotundus x x x PPolysiphonia denudata x x x x x x x x APolysiphonia elongata x x x x x x x x PPolysiphonia flexicaulis x x x PPolysiphonia harveyi x x x x x x x x APolysiphonia lanosa x x PPolysiphonia nigra x x x x x x P(?)Polysiphonia nigrescens x x x x x PPolysiphonia novae-angliae x P(?)Polysiphonia subtilissima x x x x x x x x PPolysiphonia urceolata x x PPorphyra leucosticta x x APorphyra linearis x APorphyra miniata x x x APorphyra umbilicalis x x x x x x APorphyra umbilicalis forma epiphytica x x x APorphyrodiscus simulans x P(?)Pterothamnion plumula x x x AAPtilota serrata x PRhodomela confervoides x x PRhodophysema elegans x x x PRhodophysema georgii x x P(?)Sacheria fucina x x x x x PScagelia corallina x x AATrailliella intricata x P

Total Rhodophyta Taxa 71 60 47 17 10 15 21 3 14 0

Grand Total Seaweed Taxa 144 132 90 38 26 29 49 16 30 4

Pisc

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Summary of seaweed species composition (continued)TABLE J-1

271

Acnida cannabina Water hempAster subulatus Salt marsh aster

(annual)Aster tenuifolius Salt marsh aster

(Perennial)Atriplex glabriuscula OrachAtriplex patula OrachBassia hirsuta Hairy smotherweedCarex scoparia SedgeCarex hormathodes Marsh straw sedgeCladium mariscoides Twig rushDistichlis spicata Spike grassEleocharis halophila Salt marsh spike-rushEleocharis parvula Dwarf spike-rushEleocharis smallii Small’s spike-rushElymus virginicus Virginia rye grassEuphorbia polygonifolia Seaside spurgeGerardia maritima Seaside gerardiaGlaux maritima Sea milkwortHordeum jubatum Squirrel-tail grassIva frutescens Marsh elderJuncus balticus Baltic rushJuncus canadensis Canadian rushJuncus gerardii Black grassLathyrus japonicus Beach peaLimonium nashii Sea lavenderLythrum salicaria Purple loosestrifeMyrica pensylvanica Northern bayberryPanicum virgatum SwitchgrassPhragmites australis Common reedPlantago maritima Seaside plantainPolygonum aviculare KnotweedPolygonum

ramosissimum Bushy knotweedPotamogeton pectinatus Sago pondweedPrunus maritima Beach plumPuccinellia maritima Seashore alkali grassPuccinellia paupercula Alkali grassQuercus alba White oak

Quercus bicolor Swamp white oakRanunculus cymbalaria Seaside crowfootRosa rugosa Rugosa roseRosa virginiana Low roseRuppia maritima Widgeon grassSanguisorba canadensis Canadian burnetSalicornia bigelovii Dwarf glasswortSalicornia europaea Common glasswortSalicornia virginica Perennial glasswortScirpus americanus Three-square bulrushScirpus acutus Hard-stemmed

bulrushScirpus atrovirens BulrushScirpus cyperinus Wool grassScirpus maritimus Salt marsh bulrushScirpus paludosus Bayonet-grassScirpus robustus Salt marsh bulrushScirpus validus Soft-stemmed

bulrushSmilax rotundifolia Common greenbrierSolidago sempervirens Seaside goldenrodSpartina alterniflora Salt water cord grassSpartina patens Salt meadow grassSpartina pectinata Freshwater cord grassSpergularia canadensis Common

sand spurreySpergularia marina Salt marsh

sand spurreySuaeda linearis Sea bliteSuaeda maritima Sea bliteSuaeda richii Sea bliteToxicodendron radicans Poison ivyTriglochin maritima Seaside arrow grassTypha angustifolia Narrow-leaved

cattailTypha latifolia Broad-leaved cattailZannichellia palustris Horned pondweedZostera marina Eelgrass

Major plant species occurring within New Hampshire salt marshes (modified from Breeding et al. 1974). TABLE J-2