1

FRESHWATER FISH COMMUNITIES Draft – April 2017

1. OVERVIEW Freshwater fish are ecologically important in stream ecosystems, and they provide people with significant food, recreation, and conservation value as biological indicator of freshwater streams. Historically, the streams and rivers of southern New England supported moderately diverse and abundant assemblages of native fishes. Climate change and land development are strongly affecting freshwater habitats by altering flow patterns and warming the water, which can reduce the abundance of fish species that need cold or cool (referred through this chapter as cold-coolwater fish species) and/or flowing water for some or all of their life cycle. Consequently, the relative abundance of these cold-coolwater and fluvial fish serves as an indicator of ecosystem condition. For example, brook trout (Salvelinus fontinalis) is a cold-water, fluvial species that is highly valued for conservation and recreation. The presence of brook trout and other cold-coolwater, fluvial species is indicative of good environmental health, and their distribution within the watershed provides a benchmark for the development of a robust indicator such as an index of biological integrity. In the Narragansett Bay watershed, the Palmer River had the lowest percent relative abundance of cold-coolwater (11 percent) and fluvial (9 percent) fish species. The Upper Blackstone River had the highest at 69 percent (cold-coolwater) and 67 percent (fluvial). In the Little Narragansett Bay watershed, the percent relative abundances were lowest in the Wood River, which had 30 percent cold-coolwater and 18 percent fluvial, and highest in the Lower Pawcatuck River (60 percent, 57 percent). The Southwest Coastal Ponds watershed had 21 percent cold-coolwater fish and 15 percent fluvial fish. Brook trout habitat is largely concentrated in the Lower Blackstone River and the Pawtuxet River, along catchment areas covering over 25 percent of those two watersheds. 2. INTRODUCTION

A. Fish Communities Freshwater fish are ecologically important in stream ecosystems and provide significant value to humans. Ecosystem services supported by fish include the regulation of food web dynamics and recycling of nutrients, linkages within aquatic systems and to terrestrial ecosystems, food production, recreational activities, and information services, including indicators of ecosystem stress and resilience (Holmlund and Hammer 1999). As indicators of stress, fish assemblages may provide evidence of impairment that differs from the signals provided by algae or benthic invertebrates (Carlisle et al. 2008) and is therefore important information for managing watersheds. Historically, the streams and rivers of southern New England supported moderately diverse and abundant assemblages of native fish communities. Enser and Lundgren (2005) noted that in Rhode Island, the upstream reaches of streams and rivers are fairly steep and cold, with narrow, shallow streambeds characterized by well-defined riffles and pools, and mixed bedrock, boulder, and cobble substrate; characteristic fish include brook trout, longnose dace (Rhinichthys cataractae), and blacknose dace (Rhinichthys atratulus). Downstream reaches of streams and rivers tend to be wider and sluggish, with sand and silt substrate, and native fish including pumpkinseed (Lepomis gibbosus), chain pickerel (Esox niger), and yellow perch (Perca flavescens).

2

Stream and river habitats are affected by stressors including climate change and land use, both of which can alter flow and increase water temperatures (Kanno and Vokou 2010, Beauchene et al. 2014, Bain and Meixler 2000, Kashiwagi and Richards 2009, Bain 2011, Meixler 2011). Among the land use stressors affecting streams and rivers are nutrient enrichment, toxic chemicals, and road salts. Hydrologic alterations from dams, channel modifications, shoreline stabilization, and other in-stream activities can alter flow, causing shifts in fish species composition and abundance (Carlisle et al. 2010, Poff and Zimmerman 2010). Freshwater fish assemblages are known to change in characteristic ways in response to stressors, and those changes can be used as indicators of stream and river health and integrity. Managers may use an index of biotic integrity (IBI) or a multi-metric index (MMI) to quantify aspects of the fish assemblage that are expected to respond to stressors (Whittier et al. 2007, Stoddard et al. 2008). In both approaches, metrics are calculated and then combined into a final score, which can then be related to a class of impairment. Rhode Island has not adopted an index approach but does have information on the sensitivity of fish communities to temperature and flow (RIDEM 2012, Rashleigh et al. 2013). Massachusetts and Connecticut have applied multi-metric indices to understand relationships between fish assemblage characteristics and anthropogenic factors, including temperature, flow, and other environmental, land use, and physical watershed characteristics (Armstrong et al. 2011, Bassar et al. 2016, Kanno et al. 2010, Kanno and Vokoum 2010). The states’ approaches differ, and there is no clear choice for adopting a multi-metric indicator for the entire Narragansett Bay watershed. For this report, we used two metrics that are used in all three states: percent relative abundance of cold-cool water fish and percent relative abundance of fluvial fish. Fluvial fish require flowing water for some or all of their life cycle. Coordination among the three states in the watershed could result in the development of a multi-metric index for the watershed.

B. Brook Trout Habitat Eastern brook trout, in the salmon family, has received special attention in the region due to its economic, recreational, ecological and cultural value. Brook trout primarily eat insects, and they spawn in cold-water streams in the fall. Then adults migrate to deeper waters to overwinter, and eggs hatch in the spring. Sea-run brook trout have been documented in New England, but it is unclear whether any remain in the Narragansett Bay watershed. In pre-colonial times, brook trout were present in nearly every cold-water stream and river in the eastern United States. As land clearing took place for agriculture and timber harvesting, the amount of sediment entering streams increased, and wild brook trout began to disappear (Eastern Brook Trout Joint Venture, undated). The Narragansett Bay watershed’s main streams and rivers, such as the Blackstone River, were channelized and dammed, reducing brook trout habitat through altered hydrology and pollution from industrialization activities. Many of these threats to brook trout persist today. Brook trout are known to be highly sensitive to multiple stressors, including increased temperatures, land use, and flow alteration. DeWeber and Wagner (2015) found a negative response of eastern brook trout to increasing temperature and agricultural land cover. Brook trout are found in perennial streams with temperatures between 34 and 72 °F (1 to 22°C) (Xu. et al. 2010). Bassar et al. (2016) demonstrated that declines in brook trout in western Massachusetts were related to changes in temperature and stream flow. Brook trout are particularly important ecological indicators for the region, as the Narragansett Bay watershed is near the limit of their thermal tolerance, and climate change may have a significant effect

3

on their distribution and abundance. In addition to brook trout, other fish species common in the Narragansett Bay watershed rely on cold-water stream and riparian habitats to meet one or more of their life history requirements (Massachusetts Division of Fisheries and Wildlife 2017). Thus, protecting these habitats from current and future anthropogenic and climate change stressors is critical. A decline in the brook trout population indicates negative changes in the habitat and overall ecosystem integrity. In Massachusetts, the Division of Fisheries and Wildlife maintains a list of waters that are identified as Coldwater Fishery Resources. At the regional level, brook trout status has been assessed across its range from Maine to Georgia by the Eastern Brook Trout Joint Venture (EBTJV), a partnership among state and federal agencies, regional and local governments, businesses, conservation organizations, academia, scientific societies, and private citizens working toward protecting, restoring, and enhancing brook trout populations and their habitats across their native range. Hudy et al. (2008) and the EBTJV (undated) described an array of analyses comparing current distributions to the native range, as defined by MacCrimmon and Campbell (1969). In Connecticut and Rhode Island, researchers concluded that remaining populations are small and fragmented. We used data from the EBTJV to calculate total extent, percent, and total square miles of brook trout habitat within the watershed. The information presented in this chapter represents a coordinated effort across the states within the Narragansett Bay watershed and also represents a consensus of the best professional judgment accepted by scientists and managers. 3. METHODS

A. Fish Communities The Narragansett Bay Estuary Program and the U.S. Environmental Protection Agency (Narragansett Lab) gathered, diagnosed, and reconciled fish sampling data from Massachusetts, Rhode Island, and Connecticut for this analysis. Other data sources were considered, but issues related to inconsistencies, geographical coverage, or availability made them unsuitable for this analysis. Localized studies have been conducted within the watershed, but those data were not readily available. National datasets such as the National Aquatic Resources Survey were also available, but only a limited number of the sampling sites were located within the Narragansett Bay watershed and the other two study areas, the watersheds for Little Narragansett Bay and Southwest Coastal Ponds. The fish data from Rhode Island, Massachusetts, and Connecticut were assumed to be comparable in terms of methods, as all three states used single-pass backpack shocking in the upstream direction, sampled all habitats, covered similar lengths of stream (at least 100 meters), and had similar sampling schedules (typically late spring to fall). Data were obtained from the Rhode Island Department of Environmental Management (RIDEM) Division of Fish and Wildlife (Libby 2004, Libby 2013), Massachusetts Division of Fish and Wildlife (MDFW 2014), and Connecticut Department of Energy and Environmental Protection (Hagstrom et al. 1996, Machowski and Hagstrom 2015). Data from Connecticut were included to analyze this indicator within Little Narragansett Bay watershed. For Rhode Island, samples ranged in date from April 29, 1992, to September 30, 2009, with a median date of August 26, 1999; most of the data were collected as part of a multi-year statewide survey of fish communities in rivers and streams conducted between 1992 and 2002, and survey work continued on a less frequent basis after 2002. For Massachusetts, sample dates ranged from September 21, 1994, to October 14, 2014, with a median

4

date of August 8, 2006. For Connecticut, sample dates ranged from June 14, 1993, to August 6, 2014, with a median date of February 28, 2006. In all three states’ datasets, fish collected in the field had been identified to species and abundance recorded. We used data from 2002 to 2014 in our analysis; we limited the range of years used for analysis for consistency with other reports and to enhance comparability. Due to limited repeat sampling in the dataset, it was not possible to conduct a trend analysis to identify changes in the fish communities over time. In accordance with standard practice, we adjusted the compiled dataset by removing stocked salmonids—rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar), and brown trout (Salmo trutta)—because their presence is due exclusively to stocking (Kanno and Volkun 2010, Bellucci et al. 2011, Libby 2013). Species predominantly associated with marine habitats such as mummichog (Fundulus heteroclitus) and anadromous fishes such as alewife (Alosa pseudoharengus), blueback herring (Alosa aestivalis), shad (Alosa sapidissima, Alosa mediocris), striped bass (Morone saxatilis), and sea lamprey (Petromyzon marinus) were also removed (Meixler 2011, Armstrong et al. 2011), although their abundances were very low in the samples so their inclusion would not likely have changed the results. Any hybrids or specimens not identified to species were also dropped. We calculated two metrics of the fish community that are used by both Massachusetts and Connecticut: (a) the percent relative abundance of cold-coolwater fish and (b) the percent relative abundance of fluvial fish (Table 1). This analytical approach was also supported by RIDEM. Higher values of the metrics indicate better water quality and aquatic habitat. Cold and cool-water designations for species were obtained from Kanno et al. (2010, Appendix 1). Fluvial designations for species were derived from Armstrong et al. (2011), where fluvial dependents and specialists are fish species that require flowing water for some or all, respectively, of their life cycle. In our analyses, cold- and cold-water fish were combined into a single group termed cold-coolwater fish, and fluvial dependents and specialists were combined into a single group termed fluvial fish (Table 1). In some cases, Kanno et al. (2010) presented different information regarding fluvial designations of fish species. However, we followed the designations used by Armstrong et al. (2011) in Massachusetts because most of the Narragansett Bay watershed is located within Massachusetts. The metrics were calculated as:

(Abundance of Cold-coolwater Fish/Total Fish Abundance) 100

(Abundance of Fluvial Fish/Total Fish Abundance) 100 Abundance was defined as the number of individuals. We note that Armstrong et al. (2011) reported relative abundance as counts per hour, so these methods are not directly comparable. We used geographical information systems (GIS) tools in ArcGIS desktop (ESRI 2016) to associate the latitude and longitude reported by the states for each sample site were used with a HUC10 watershed. For the Southwest Coastal Ponds, metrics were summarized at the HUC12 subwatershed level, as the entire area is encompassed by one HUC10 watershed. Within each HUC10 watershed or HUC12 subwatershed, we calculated the average of percent relative abundance for each group: cold-coolwater and fluvial fish.

5

Table 1. Freshwater fish species of the Narragansett Bay watershed and their requirements for cold/cool water temperatures, flowing water (fluvial), or both.

Common Name Scientific Name Cold-coolwater Fish Fluvial Fish5

American Brook Lamprey1 Lethenteron appendix Cold Specialist Blacknose Dace2 Rhinichthys atratulus Cool Specialist Brook Trout Salvelinus fontinalis Cold Specialist Common Shiner Luxilus cornutus Cool Dependent Creek Chub2 Semotilus atromaculatus Cool Specialist Creek Chubsucker Erimyzon oblongus Specialist Fallfish Semotilus corporalis Cool Specialist Fourspine Stickleback3 Apeltes quadracus Cool Dependent Longnose Dace Rhinichthys cataractae Cool Specialist Rock Bass4 Ambloplites rupestris Cool Smallmouth Bass4 Micropterus dolomieu Cool Tesselated Darter Etheostoma olmstedi Cool Specialist White Perch Morone americana Cool White Sucker2 Catostomus commersoni Cool Dependent Yellow Perch Perca flavescens Cool

1 Brook lamprey was not categorized by Armstrong et al. (2011) but was considered a fluvial specialist by Kanno (2010). 2 These species are considered tolerant to pollution (Halliwell et al. 1999), so they may be present in areas of low quality despite their specialized habitat requirements. Kanno et al. (2010) developed a metric that omitted blacknose dace. However, Armstrong et al. (2010) demonstrated strong relationships between flow and dace, so we included this species. Also, Kanno et al. (2010) included a metric for white sucker that is expected to be higher in more degraded areas. 3 The dataset included fourspine stickleback, which is primarily a saltwater or brackish-water fish but is often found in freshwater. The species is very rare in the Narragansett Bay watershed and did not strongly affect results. 4 These species are considered nonnative. Some assessment approaches exclude nonnative species, as their presence may not be desirable. The abundance of these species was extremely low and did not strongly affect results. 5 Fluvial dependents and specialists are fish species that require flowing water for some or all, respectively, of their life cycle. In analyses, the two categories are combined into a single group termed fluvial fish.

B. Brook Trout Habitat We report on the amount of brook trout habitat because this habitat is indicative of sensitive areas for watershed protection to sustain cold-coolwater aquatic ecosystems. To this end, we obtained data on brook trout habitat patches from the Eastern Brook Trout Joint Venture (EBTJV 2015). In 2015, the EBTJV performed a habitat patch analysis coordinated across states at a regional scale, including the Narragansett Bay watershed, to identify catchment areas of rivers and streams with presence of brook trout in the previous two decades. We used these data as a proxy to identify potential presence of brook trout and thus available habitat. The EBTJV methodology for the salmonid catchment assessment and habitat patch layers was described in Coombs and Nislow (2015). The salmonid catchment assessment and habitat patch layers were created using algorithms for spatial data analysis performed on an ArcGIS platform. The geospatial analysis used fish data from different Joint Venture partners from each state, the National Hydrography Dataset (NHD+ version 2, McKay et al. 2012), and the National Anthropogenic Barrier Dataset to define areas where brook trout was at least once observed. The Estuary Program utilized the EBTJV’s brook trout patch layers within the Narragansett Bay watershed as well as within the Little Narragansett Bay and Southwest Coastal Ponds watersheds. In

6

order to exclude introduced or stocked species from the analysis, we included brook trout only and removed others (brown, rainbow, and stocked trout) from the dataset. We used all habitat patches, both observed and predicted, that had been identified by the EBTJV. For each HUC10 watershed or HUC12 subwatershed, we calculated brook trout habitat as the total area in square miles and percent of each watershed or subwatershed. It is important to note that habitat patch areas encompassed the entire extent of a catchment area of streams and rivers where fish sampling took place and brook trout was observed, and not only natural buffers. In the context of habitat protection, these catchment areas are important for watershed characterization, and while it is expected that sampling of brook trout from decades ago might not represent today’s conditions, the areas defined by EBTJV are of great importance to target restoration activities for protection of potential habitat and conservation of brook trout communities. Moreover, it is assumed that current floodplains, freshwater wetlands, and overall riparian buffers along the streams within the brook trout habitat patches are ecologically significant for protecting cold-water habitat. 4. STATUS

A. Narragansett Bay

i. Fish Communities In the Narragansett Bay watershed, the percent relative abundance of cold-coolwater species ranged from 11 percent in the Palmer River to 67 percent in the Upper Blackstone River (Table 2). Percent relative abundance of fluvial species ranged from 9 percent in the Palmer River to 65 percent in the Upper Blackstone River (Table 2). The two metrics are highly correlated (r=0.91), and the data are quite variable. Figure 1 plots the percent relative abundance of cold-coolwater and fluvial fish, and shows that the data are skewed, as the medians are quite different from the means (diamonds) within each HUC10 watershed and as compared among watersheds. The range of data for both metrics within the full Narragansett Bay watershed was 0-100 percent. Table 2. Average of percent relative abundance for cold-coolwater fish and fluvial fish by HUC10 in the Narragansett Bay watershed. SD = standard deviation.

HUC10 Name HUC10 No. Samples Average Cold-

coolwater Fish % (SD) Average Fluvial

Fish % (SD)

Upper Blackstone River 0109000301 69 67 (36) 65 (38)

Lower Blackstone River 0109000302 70 50 (38) 46 (41)

Upper Taunton River 0109000401 19 22 (28) 22 (28)

Middle Taunton River 0109000402 55 32 (32) 30 (32)

Threemile River 0109000403 16 28 (34) 29 (34)

Ten Mile River 0109000404 18 20 (30) 18 (30)

Woonasquatucket River-Moshassuck River

0109000405 0 - -

Pawtuxet River 0109000406 12 25 (17) 18 (33)

Palmer River 0109000407 32 11 (22) 9 (17)

Lower Taunton River-Frontal Mount Hope Bay

0109000408 37 15 (37) 16 (23)

Narragansett Bay 0109000409 54 31 (37) 24 (36)

7

Figure 1. Percent relative abundance of cold-coolwater fish and fluvial fish within HUC10 watersheds in the Narragansett Bay watershed. HUCs are represented by the last 3 digits of their number, see Table 2 for HUC numbers and names. Horizontal lines indicate medians. Boxes represent the 25th percentile to 75th percentile. Whiskers indicate the range, means shown as open diamonds, solid points are outliers.

ii. Brook Trout Habitat The analysis indicated that 14.5 percent of the total Narragansett Bay watershed area potentially provides suitable habitat for brook trout. Brook trout habitat areas within the HUC10 watersheds (Figure 2) range from 0 percent in the Ten Mile River and Upper Taunton River to 29.3 percent in the Pawtuxet River (Table 3). Table 3. Predicted or potential brook trout habitat within HUC10 watersheds in the Narragansett Bay watershed. Sorted by highest to lowest percentage of brook trout habitat.

Watershed Name HUC10 Brook Trout Habitat within

Watershed

Percent Square miles

Pawtuxet River 0109000406 29.3 175.7 Lower Blackstone River 0109000302 27.0 188.0 Middle Taunton River 0109000402 21.3 99.2 Upper Blackstone River 0109000301 12.4 65.8 Narragansett Bay 0109000409 10.6 66.4 Woonasquatucket River-Moshassuck River 0109000405 6.2 11.9 Lower Taunton River-Frontal Mount Hope Bay 0109000408 5.9 24.1 Threemile River 0109000403 3.2 7.0 Palmer River 0109000407 1.4 2.5 Upper Taunton River 0109000401 0.0 0.0 Ten Mile River 0109000404 0.0 0.0

8

Figure 2. Percentage brook trout habitat (dark green areas) in HUC10 watersheds in the Narragansett Bay watershed.

9

B. Little Narragansett Bay

i. Fish Communities In the Little Narragansett Bay watershed, the percent relative abundance of cold-coolwater species ranged from 30 percent in the Wood River to 60 percent in the Lower Pawcatuck River. The percent relative abundance of fluvial species ranged from 18 percent in the Wood River to 57 percent in the Lower Pawcatuck River (Table 4). The three headwaters HUC10s had similar values to one another. Unlike in the Narragansett Bay watershed, the HUC10 located farthest downstream had the highest metric values. Figure 3 plots the percent relative abundance of cold-coolwater and fluvial fish for the Little Narragansett Bay and Southwest Coastal Ponds (represented as 504) watersheds, and shows that the data are skewed, as the medians are quite different from the means (diamonds) – an exception for the cold-coolwater metric for the Upper Pawcatuck River (represented as 502) – within each HUC10 watershed and as compared among HUC10 watersheds. Table 4. Average of percent relative abundance for cold-coolwater fish and fluvial fish by HUC10 in the Little Narragansett Bay watershed. SD = standard deviation.

Watershed Name HUC10 No.

Samples

Average Cold-coolwater Fish %

(SD)

Average Fluvial Fish % (SD)

Wood River 0109000501 6 30 (37) 18 (33)

Upper Pawcatuck River 0109000502 26 34 (30) 27 (29)

Lower Pawcatuck River 0109000503 65 60 (37) 57 (38)

Part of Southeast Coastal-Pawcatuck River to Eastern Point

0110000303 No Data1 - -

1 The Estuary Program will incorporate data from Connecticut in future assessments.

Figure 3. Percent relative abundance of cold-coolwater fish and fluvial fish within HUC10 watersheds of the Little Narragansett Bay and Southwest Coastal Ponds watersheds. HUCs are represented by the last 3 digits of their number, see Table 4 for HUC numbers and names (Southwest Coastal Ponds is

10

represented as 504). Horizontal lines indicate medians. Boxes represent the 25th percentile to 75th percentile. Whiskers indicate the range, means shown as open diamonds, solid points are outliers.

ii. Brook Trout Habitat In the Little Narragansett Bay watershed, the analysis identified 46 percent of the total area as habitat for brook trout. The HUC10 watersheds ranged from 43 percent to 66 percent brook trout habitat (Table 5 and Figure 4). Table 5. Predicted or potential brook trout habitat within HUC10 watersheds in Little Narragansett Bay watershed. Sorted by highest to lowest percent of brook trout habitat.

Watershed Name HUC10 Brook Trout Habitat within

Watershed

Percent Square miles

Part of Southeast Coastal-Pawcatuck River to Eastern Point

0110000303 65.7 10.0

Lower Pawcatuck River 0109000503 57.4 34.0 Wood River 0109000501 42.9 38.5 Upper Pawcatuck River 0109000502 42.8 65.5

11

Figure 4. Percentage brook trout habitat (dark green areas) in HUC10 watersheds in the Little Narragansett Bay watershed.

12

C. Southwest Coastal Ponds

i. Fish Communities In the three HUC12 subwatersheds in the Southwest Coastal Ponds watershed, Saugatucket River had 36 percent relative abundance for both cold-coolwater fish and fluvial fish, primarily due to brook trout and tessellated darter, and Ninigret Pond-Front Block Island Sound had 19 percent cold-coolwater fish and 14 percent fluvial fish, primarily due to brook trout (Table 6). No fish data were recorded for the Point Judith Pond-Frontal Block Island Sound subwatershed. Table 6. Average of percent relative abundance for cold-coolwater fish and fluvial fish in subwatersheds of the Southwest Coastal Ponds watershed. SD = standard deviation.

Subwatershed Name HUC12 No.

Samples Average Cold-

coolwater Fish % (SD)

Average Fluvial Fish % (SD)

Saugatucket River 010900050401 1 36 (N/A) 36 (N/A)

Point Judith Pond-Frontal Block Island Sound

010900050402 No Data1 - -

Ninigret Pond-Frontal Block Island Sound

010900050403 13 19 (30.7) 14 (30.3)

Watershed Name HUC10

Frontal Block Island Sound 0109000504 14 21 (29) 15 (30) 1 There were no fish sampling stations within this subwatershed.

ii. Brook Trout Habitat Overall, 27.4 percent of the area within the Southwest Coastal Ponds watershed could potentially provide habitat for brook trout, ranging from 13 percent to 40 percent within the HUC12 subwatersheds (Table 7 and Figure 5). Table 7. Predicted or potential brook trout habitat in the Southwest Coastal Ponds watershed. Sorted by highest to lowest percent of brook trout habitat.

Subwatershed Name HUC12 Brook Trout Habitat within

HUC10 or HUC12

Percent Square miles

Saugatucket River 010900050401 40.4 6.9 Ninigret Pond-Frontal Block Island Sound 010900050403 24.9 6.9 Point Judith Pond-Frontal Block Island Sound 010900050402 13.3 1.5

Watershed Name HUC10

Frontal Block Island Sound 00109000504 27.4 15.4

13

Figure 5. Percentage brook trout habitat (dark green areas) within HUC12 subwatersheds in the Southwest Coastal Ponds watershed.

5. DISCUSSION

A. Fish Communities The large range of values (0 to 100 percent) observed for both the cold-coolwater fish and fluvial fish metrics indicates that they are useful and sensitive for the study area (Whittier et al. 2007). At one extreme, sites that support only brook trout would show 100 percent for both metrics. A threshold may be selected to separate out predominantly brook trout sites (e.g., >90 percent fluvial fish), which would be similar to other states (e.g., NHDES 2007, Kanno et al. 2010). Cold and cool water streams are recognized by Rhode Island and Massachusetts as valuable habitats and managed accordingly. At the other extreme, some sites showed zero percent of both cold-coolwater fish and fluvial fish. A threshold could also be set to separate sites with few or no fluvial fish (e.g., <10 percent fluvial fish), which may be located near the coast. The results indicate that impairment may vary by subwatershed. For comparison, Kashiwagi and Richards (2009) considered that a target, or reference, fish community for the Blackstone River should contain 51 percent fluvial specialists and 26 percent fluvial dependents, for a total of 77 percent fluvial fish. The results of our analysis for the upper (65 percent) and lower (46 percent) Blackstone River indicated some difference from this target (Table 2). Similarly, Kashiwagi and Richards (2009)

14

estimated 76 percent fluvial species in the target fish community for the Taunton River, and our results showed 22 and 30 percent for the upper and middle Taunton, respectively (Table 2). The Wood River was used as a reference condition in the Kashiwagi and Richards (2009) report, and the percentage was reported as 67 percent fluvial fish, which was much higher than our result of 18 percent (Table 4). Similarly, Kashiwagi and Richards (2009) estimated 56 percent fluvial fish for the Pawcatuck River, which is consistent with the 57 percent in our results for the Lower Pawcatuck River (Table 4). Across the HUC10 watersheds, the spatial patterns of the results for abundance of cold-coolwater fish and fluvial fish were not surprising. Both measures were higher in upper reaches of the watershed, likely due to both elevation and development patterns. Enser and Lundgren (2005) noted that in Rhode Island, upper reaches of streams and rivers are fairly steep and cold, whereas lower stream and river reaches may be warmer and slower due to reduced elevation gradients. Although the absence of cold-coolwater and fluvial species may be due to stressors (e.g., urban development) or environmental setting (e.g., coastal streams), or a combination of the two, the presence of these species is indicative of good environmental health, and their distribution within the study area provides a benchmark for future assessment. The high correlation of the cold-coolwater and fluvial metrics of relative abundance is expected, because in many cases the species that make up these metrics are both cool water and fluvial (Table 1). In their IBI development, the state of New Hampshire used a cutoff point of 0.8 Spearman correlation coefficient as a threshold for strong correlation (NHDES 2007), so both metrics would likely not be used together in an index. Similarly, the percent of warm-water species would be the complement of the cold-coolwater species. While the streams in the Narragansett Bay watershed can be expected to support both cold-coolwater and warm-water fisheries, impairment due to stressors can shift the composition toward warm-water fisheries (e.g., Flanagan et al. 1999). Some additional metrics could be considered for analysis. Trophic and tolerance metrics are often used in assessments, although Bain (2010) found that aspects of fish species tolerance were less responsive than habitat in the Quinebaug River in Massachusetts. Coles et al. (1995) found that cyprinid species were sensitive to urbanization in New England coastal streams; Kanno et al. (2010) also included cyprinid species in their MMI. Introduced species may also be indicators for impaired streams, particularly those species in the family Centrarchidae (e.g., Bain and Meixler 2000, Bain 2010). The Estuary Program may be able to add unique value by continuing to review, test, and coordinate the varied state approaches. These metrics can be related to the Biological Condition Gradient framework, and in particular it may be useful to relate the fluvial fish metric to the land use stressor (i.e., percent of urban lands, impervious cover, forested lands).

B. Brook Trout Habitat While these results only offer a preliminary view of habitats that support brook trout or could have supported it at the time when data were collected and analyzed, this provides an opportunity to reassess these catchment areas in a holistic fashion, by continuing to collect fish data and defining new or existing areas where conditions are suitable for cold-water species. Conditions of the contributing areas could have changed over the last 10 or more years—due to land use changes, habitat fragmentation, and degraded water quality—which constrain the results to being only an estimation of potential habitat.

15

EBTJV habitat patches across the watersheds of Narragansett Bay, Little Narragansett Bay, and the Southwest Coastal Ponds indicated remaining habitat areas that should be protected for maintaining cold-coolwater streams that support brook trout and other cold-coolwater species. Although brook trout have been studied within the Wood-Pawcatuck watershed (Tefft 2013), to our knowledge brook trout distributions have not been considered at the scale of the Narragansett Bay watershed. On the other hand, the percentage area of brook trout habitat was used as metric in this report, the results should not be directly compared with those by the Eastern Brook Trout Joint Venture, as our methods were developed based on best professional judgement which used EBTJV as secondary data. One of the applications of comparing designated cold-water stream habitat to brook trout predicted habitat and actual observations of brook trout from monitoring is to guide managers and partners in locating specific areas to assess water and habitat quality and to prioritize research and management efforts. While the Narragansett Bay watershed is not the primary core habitat area for brook trout in the New England region, this analysis showed that the subwatersheds can support core habitat that could contribute significantly to conservation of brook trout and other cold-coolwater species. Given that over 25 percent of the area of the Pawtuxet River and Lower Blackstone River subwatersheds have been mapped as brook trout habitat patches by the EBTJV and estimated by the Estuary Program as important areas for protection of cold-water habitat and the conservation of brook trout, these areas seem to align with other watershed indicators and characteristics examined by the Estuary Program such as low levels of urban development (see “Land Use” and “Impervious Cover” chapters) and larger natural areas (see “Land Use” chapter) that are identified as ecologically significant for watershed protection and also protected as open space (see “Open Space” chapter). 6. DATA GAPS AND RESEARCH NEEDS Ongoing collection of freshwater fish assemblage data is needed, particularly for Rhode Island, where recent data are lacking. Targeted collection of data on brook trout could better refine the brook trout habitat predictions and clarify cold-water stream designations. Additional considerations of data collection to support trends analysis could be discussed among the states. For example, certain subwatersheds had fewer samples (e.g., Woonasquatucket River-Moshassuck River). Some additional freshwater habitats that were not considered here but may be within brook trout catchment areas and have ecological significance for fish include intermittent streams, blackwater creeks, freshwater reaches of tidal rivers, lakes, ponds, wetlands, peatlands, and bogs (Enser and Londgren 2006). Specialized methods for collection of fishes in these habitats may need to be identified or developed. Additional efforts are needed to characterize diadromous fish, which are those species that live the majority of their lives in either freshwater or saltwater and then migrate to the opposite water type to spawn. The state field surveys were not designed to sample diadromous species, which are likely underrepresented in the data. Additional attention may be needed for anadromous fish (those spawning in freshwater), including river herring (alewife and blueback herring), Atlantic salmon, rainbow smelt, sturgeon, and American shad, as well as the catadromous American eel (which spawns in saltwater). In particular, the Nemasket River in the Taunton River Basin supports the largest alewife fish run in the state of Massachusetts (Bowden 2013), and sturgeon—a rare, large, native species—has been found in the lower Taunton River. Collection and/or prediction of environmental data that coordinates with fish data is also needed. Specifically, more information is needed on stream flow, water withdrawals, stream temperature, stream barriers, riparian buffers, water quality, and overall aquatic habitat. In-stream temperature

16

monitoring is an important data gap. Many states have instituted continuous monitoring of temperature in order to provide resource managers with needed information on the potential effects of various stressors on riverine ecosystems. To our knowledge, there is currently very limited data collection of this type within the Narragansett Bay watershed (see “Temperature” chapter). In addition to its value for assessing landscape stressors, water temperature monitoring in rivers and streams over time is needed to discern and understand potential impacts of a changing climate. Future analysis will explore and quantify the relationships between ecological metrics, including those presented here, and environmental data at multiple scales (e.g., site, watershed, catchment areas), including multiple stressors such as percent of impervious cover, stream flow, water withdrawals, stream temperature, conditions of stream barriers, and riparian buffer characteristics. For example, Armstrong et al. (2011) quantified the reduction in fluvial fish abundance in Massachusetts in response to percent depletion of August median flow and impervious cover. Methods for these analyses could include empirical and regression approaches (e.g. Freeman and Marcinek 2006, Kanno and Vokoun 2010), as well as threshold analysis, which was used in Connecticut (Beauchene et al. 2014). Bayesian regression approaches could allow for the inclusion of different datasets (e.g., national data, targeted local studies) and updates as additional data are collected. For brook trout specifically, important next steps are data collection and integration to support the improvement and update of the Eastern Brook Trout Joint Venture Salmonid Catchment Assessment and Habitat Patch Layers model to continue tracking these critical areas over time. There are significant ongoing regional research efforts on brook trout through the Eastern Brook Trout Joint Venture, Trout Unlimited, U.S. Geological Survey Conte Anadromous Fish Branch, Massachusetts Cooperative Fish and Wildlife Unit, and state partners that are addressing research questions related to expected changes in and effects of water temperature, flow, and land use, and aspects of conservation. Future research in the Narragansett Bay watershed will coordinate with these ongoing efforts and will seek to use available regional research results in watershed assessment and management. An understanding of how stressors affect indicators can be used to support development and validation of management tools such as state-level indices (i.e., for Rhode Island) and coordination of freshwater fish indices across the Narragansett Bay watershed. These tools would strengthen the water quality assessment process by incorporating a second biological indicator and providing an improved tool for tracking change over time (RIDEM, personal communication). Longer-term development of indicators for freshwater fish may involve either the development of an IBI or MMI for the Narragansett Bay watershed. The environmental state practitioners in Rhode Island would like an index for their statewide monitoring and reporting responsibilities. The state data could support the development of an index following the example of Connecticut (Kanno et al. 2010) and others (e.g., Stoddard et al. 2008). These metrics can be related to the Biological Condition Gradient framework, as has been done in Connecticut (Stamp and Gerritsen 2013). An additional need is to translate these findings to support conservation and restoration. Erkan (2002) described restoration efforts for anadromous fish within the state of Rhode Island, which included improvement of passage for juveniles and adults through dam breaching and removal, installation of fishways, and removal of vegetative and debris obstructions. To support identification of priority areas for conservation and restoration activities, our findings regarding distribution of fluvial fish could be combined with the North Atlantic Aquatic Connectivity data on locations and conditions of stream

17

barriers. Habitat protection priorities identified by The Nature Conservancy also could be implemented. Noteworthy are the array of projects throughout the Narragansett Bay watershed focused on fish passage, including both assessments and implementation, and the importance of reconciling and streamlining information about aquatic habitat conditions in relation to continuity and connectivity. It would be of interest to environmental practitioners, researchers, and advocates to identify and quantify the effects of stream barriers to changes on fish assemblages through habitat fragmentation, water quality degradation, and stream flow alteration. To date, most of the restoration efforts and funding in the Narragansett Bay watershed have focused on anadromous fish (RIDEM 2002 and 2013, Foran et al. 2017, final report under review). A study led by the U.S. Army Engineer Research and Development Center (Foran et al. under review) in collaboration with partners including the Estuary Program evaluated the effect of multiple ecosystem restoration projects at the Narragansett Bay watershed level and calculated passable and unpassable fish passage. The study found that approximately 854 stream miles have been opened to anadromous fish (i.e., alewife herring, blueback herring, and shad), 435 miles to eels, and 154 miles to brook trout as a result of dam removals and other fish passage restoration projects in Rhode Island and Massachusetts. However, Foran et al. analysis stops at the upstream limits of suitable habitat for anadromous fish (RIDEM 2002 and 2013). In 2016, preliminary results from field assessments of over 400 stream barriers (i.e., culverts and bridges) in the Wood-Pawcatuck Rivers identified that 43 percent of the assessed structures provided full passage to aquatic organisms, while 57 percent were identified as moderate to severe barriers (Fuss and O’Neill 2016, final report under review). Similar research and assessments should be conducted and replicated across the watershed, which can be prioritized utilizing the findings from this report and other efforts to target areas in the watershed for habitat protection of for cold-coolwater and fluvial fish species. 7. ACKNOWLEDGEMENTS This chapter was written by Brenda Rashleigh, Assistant Laboratory Director for Water in the Safe and Sustainable Water Resources Research Program at EPA’s National Health and Environmental Effects Laboratory, and Eivy Monroy, Watershed and GIS Specialist with the Narragansett Bay Estuary Program. GIS data preparation and analyses were conducted with the GIS support of Julia Twichell and Jamie Duncan-Brown, GIS Environmental Analysts with the Estuary Program. We are grateful to RIDEM, MADFW, and CT DEEP for access to their fish data. The information in this document has been subjected to Environmental Protection Agency review and approved for publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. 8. REFERENCES Armstrong, S., T.A. Richards, and S.B. Levin. 2011. Factors influencing riverine fish assemblages in Massachusetts. U.S. Geological Survey Scientific Investigations Report 2011–5193. Bain, M.B., and M.S. Meixler. 2000. Defining a target fish community for planning and evaluating enhancement of the Quinebaug River in Massachusetts and Connecticut. Produced for: Quinebaug River Instream Flow Study Agencies.

18

Bain, M.B. 2011. Target fish communities for restoration of waterways supporting society and nature. Appl. Ichthyol. 27(Suppl. 3):86–93. Bassar, R.D, B.H. Letcher, K.H. Nislow, and A.R. Whiteley. 2016. Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout. Global Change Biology 22:577–593. Beauchene, M., M. Becker, C.J. Bellucci, N. Hagstrom, and Y. Kanno. 2014. Summer thermal thresholds of fish community transitions in Connecticut streams. North American Journal of Fisheries Management 34:119–131. Bellucci, C.J., M. Becker, and M. Beauchene. 2011. Characteristics of macroinvertebrate and fish communities from 30 least disturbed small streams in Connecticut. Northeastern Naturalist 18:411–444. Bowden, A.A. 2013. Towards a comprehensive strategy to recover river herring on the Atlantic seaboard: lessons from Pacific salmon. ICES J. Mar. Sci. doi:10.1093/icesjms/fst130. Carlisle, D.M., D.M. Wolock, and M. Meador. 2010. Alteration of streamflow magnitudes and potential ecological consequences: a multiregional assessment. Frontiers in Ecology and the Environment doi:10.1890/100053. Carlisle, D.M., C.P. Hawkins, M.R. Meador, M. Potapova, and J. Falcone. 2008. Biological assessments of Appalachian streams based on predictive models for fish, macroinvertebrate, and diatom assemblages. Journal of the North American Benthological Society 27(1):16–37. Coles, J.F., T.F. Cuffney, G. McMahon, and K.M. Beaulieu. 2004. The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams. U.S. Geological Survey Professional Paper 1695, Reston, VA. Coombs, J.A., and K.H. Nislow. 2015. EBTJV Salmonid Catchment Assessment and Habitat Patch Layers. University of Massachusetts Department of Environmental Conservation. Amherst, MA. DeWeber, J.T., and T. Wagner. 2015. Predicting brook trout occurrence in stream reaches throughout their native range in the eastern United States. Transactions of the American Fisheries Society 14:11–24. EBTJV (Eastern Brook Trout Joint Venture), undated. Eastern brook trout: status and threats. Retrieved from: http://easternbrooktrout.org/reports/eastern-brook-trout-status-and-threats/view EBTJV (Eastern Brook Trout Joint Venture), 2015. EBTJV Salmonid Catchment Assessment and Habitat Patch Layers. Data retrieved from: http://ecosheds.org:8080/geoserver/www/Web_Map_Viewer.html Energy and Environmental Affairs (EEA), Department of Environmental Protection (MassDEP), and the Department of Conservation and Recreation (DCR). 2012. Sustainable Water Management Initiative (SWMI). Retrieved from:

19

http://www.mass.gov/eea/agencies/massdep/water/watersheds/sustainable-water-management-initiative-swmi.html Enser, R.W., and J. A. Lundgren. 2006. Natural Communities of Rhode Island. A joint project of the Rhode Island Dept. of Environmental Management Natural Heritage Program and The Nature Conservancy of Rhode Island. Web published by R.I. Natural History Survey, Kingston, RI. Retrieved from: www.rinhs.org Erkan, D.E. 2002. Strategic plan for the restoration of anadromous fish to Rhode Island coastal streams. RIDEM Division of Fish and Wildlife. Retrieved from: http://www.dem.ri.gov/programs/bnatres/fishwild/pdf/riap2002.pdf ESRI, 2016. ArcGIS Desktop: Release 10.5. Environmental Systems Research Institute, Redlands, CA. Flanagan, S.M., M.G. Nielsen, K.W. Robinson, and J.F. Coles. 1999. New England coastal basins in Maine, Massachusetts, New Hampshire, and Rhode Island: Environmental settings and implications for water quality and aquatic biota. U.S. Geological Survey, Water Resources Investigations Report 98-4249. Pembroke, New Hampshire. Foran, C.M., C. Fox-Lent, C. Chadderton, W. Gendron, L. Oliver, E. Monroy, J. Turek, P. Edwards, and Suedel, B. In review. Watershed Level Effects of Multiple Ecosystem Restoration Projects. United States Army Corps of Engineers (USACE). Available upon request from Foran, C.M. U.S. Army Engineer Research and Development Center, Environmental Laboratory. Freeman, M., and P. Marcinek. 2006. Fish assemblage responses to water withdrawals and water supply reservoirs in Piedmont streams. Environmental Management 38(3):435–450. Fuss and O’Neill. 2016. Dams, Bridges and Culverts Assessment Technical Memorandum. Wood-Pawcatuck Watershed Flood Resiliency Management Plan. Wood-Pawcatuck Watershed Association. Project No. 20111470.B10. Retrieved from: http://www.wpwa.org/documents/Wood-Pawcatuck%20Dams-Bridges-Culverts%20Assessment%20October%202016.pdf Halliwell, D.B., R.W. Langdon, R.A. Daniels, J.P. Kurtenbach, and R.A. Jacobson. 1999. Classification of freshwater fish species of the northeastern United States for use in the development of indices of biological integrity, with regional applications. In: Assessing the sustainability and biological integrity of water resources using fish communities (T.P. Simon, Ed.). CRC Press, Boca Raton, FL. pp. 301–333. Hagstrom, N.T., M. Humphreys, W.A. Hyatt, and W.B. Gerrish. 1996. A survey of Connecticut streams and rivers. Federal Aid to Sport Fish Restoration. Final Report F-66-R. Connecticut Department of Environmental Protection. Holmlund, C.M., and M. Hammer. 1999. Ecosystem services generated by fish populations. Ecological Economics 29:253–268.

20

Horowitz, R.J. 1978. Temporal variability patterns and the distributional patterns of stream fishes. Ecol. Monogr. 48:307–321. Hudy, M., T.M. Thieling, N. Gillespie, and E.P. Smith. 2008. Distribution, status, and land use characteristics of subwatersheds within the native range of brook trout in the Eastern United States. North American Journal of Fisheries Management 28:1069–1085. Kashiwagi, M., and T. Richards. 2009. Development of Target Fish Community Models for Massachusetts Mainstem Rivers. Massachusetts Department of Fish and Game, Division of Fish and Wildlife. 92 pp. Kanno, Y., and J.C. Vokoun. 2010. Evaluating effects of water withdrawals and impoundments on fish assemblages in Southern New England streams, USA. Fisheries Management and Ecology (17): 272-283. Kanno, Y., J.C. Vokoun, and M. Beauchene. 2010. Development of dual fish multi-metric indices of biological condition for streams with characteristics thermal gradients and low species richness. Ecological Indicators 10:565–571. Libby, A.D. 2004. A preliminary summary of fish surveys that were conducted in Rhode Island's streams and ponds between 1993 and 2002. Research Reference Document 2004/1, Federal Aid in Sport Fish Restoration Project F-20-R. Rhode Island Department of Environmental Management, Division of Fish and Wildlife. Libby, A.D. 2013. Inland Fishes of Rhode Island. Rhode Island Department of Environmental Management, Providence, RI. 287 pp. MacCrimmon, H.R., and J.S. Campbell. 1969. World distribution of brook trout, Salvelinus fontinalis. Journal of the Fisheries Research Board of Canada 26:1699–1725. Machowski, E., and N. Hagstrom. 2015. Connecticut Inland Fisheries: Monitoring Fish Populations in Streams. Connecticut Department of Energy and Environmental Protection, Hartford, CT. Massachusetts Division of Fisheries and Wildlife. 2014. Stream Survey and Inventory Protocols. Retrieved from: http://www.mass.gov/eea/agencies/dfg/dfw/wildlife-habitat-conservation/streamsurveyinventoryprotocol.pdf Massachusetts Division of Fisheries and Wildlife. 2017. Coldwater Fish Resource (CFR). Retrieved from: http://www.mass.gov/eea/agencies/dfg/dfw/wildlife-habitat-conservation/what-is-cfr-.html McKay, L., T. Bondelid, T. Dewald, J. Johnston, R. Moore, and A. Rea. 2012. NHDPlus Version 2: User Guide. Meixler, M.S. 2011. Application of the target fish community model to an urban river system. Journal of Environmental Management 92:1138–1147.

21

New Hampshire Department of Environmental Services (NHDES). 2007. Coldwater fish assemblages index of biotic integrity for New Hampshire wadeable streams. R-WD-07-33. Concord, NH. North Atlantic Aquatic Connectivity Collaborative. Retrieved from: https://www.streamcontinuity.org/ Poff, N.L., and J.K.H. Zimmerman. 2010. Ecological responses to altered flow regimes: a literature review to inform the science and management of environmental flows. Freshwater Biology 55:194–205. Rashleigh, B., A. Richardson, M. Nimiroski, and A. Libby. 2013. Freshwater fish assemblage patterns in Rhode Island streams and rivers. Presented at: Ecological Society of America, Minneapolis, MN. Rhode Island Department of Environmental Management (RIDEM). 2012. Fish community sampling and analysis in Rhode Island rivers and streams: Data and preliminary analysis. Providence, RI. Schlosser, I.J. 1982. Fish community structure and function along two habitat gradients in a headwater stream. Ecological Monographs 52:395–414. Schlosser, I.J. 1990. Environmental variation, life history attributes, and community structure in stream fishes: implications for environmental management and assessment. Environmental Management 14(5):621–628. Stamp, J., and J. Gerritsen. 2013. A biological condition gradient (BCG) assessment model for stream fish communities of Connecticut. TetraTech Inc, Owing Mills, MD. Stoddard, J.L., A.T. Herlihy, D.V. Peck, R.M. Hughes, T.R. Whittier, and E. Tarquinio. 2008. A process for creating multimetric indices for large-scale aquatic surveys. J. N. Am. Benthol. Soc. 27:878–891. Tefft, E. 2013. Factors affecting the distribution of brook trout (Salvelinus fontinalis) in the Wood-Pawcatuck watershed of Rhode Island. University of Rhode Island, Kingston, RI. Retrieved from: http://www.edc.uri.edu/mesm/docs/majorpapers/tefft_gisrs_2013.pdf Tefft, E., and P. Edwards. 2013. Rhode Island’s Fish Passage Maintenance Guide. Rhode Island Division of Fish and Wildlife. Department of Environmental Management. Fish and Wildlife Research Reference Document #2013/1. Available upon request from RIDEM, Division of Fish and Wildlife. Whittier, T.R., R.M. Hughes, J.L. Stoddard, G.A. Lomnicky, D.V. Peck, and A.T. Herlihy. 2007. A structured approach for developing indices of biotic integrity: three examples from streams and rivers in the western USA. Trans. Am. Fish. Soc. 136:718–735.

22

Xu, C.L., B.H. Letcher, and K.H. Nislow. 2010. Size-dependent survival of brook trout Salvelinus fontinalis in summer: effects of water temperature and stream flow. Journal of Fish Biology 76(10):2342–2369.