Data Integration of WRIA 1 Hydraulic, Fish Habitat, and Hydrology

Data Integration of WRIA 1 Hydraulic, Fish Habitat, and Hydrology Models June 2013

1 | D a t a I n t e g r a t i o n o f W R I A 1 M o d e l s

June 2013

An interdisciplinary team of water resource technical specialists worked with the WRIA 1 Joint Board Staff Team and members of the WRIA 1 Instream Flow and/or Fish Habitat Technical teams to combine the results from existing and updated technical models, studies, and data into an integrated set of information to support the goals of the WRIA 1 Watershed Management Project. A complete list of contributors is included in this report. Graphic Design: Tim Sauder, asmallpercent

Technical reviewers: Jeremy Freimund, Lummi Nation; Treva Coe, Nooksack Indian Tribe; Kasey Cykler, Washington State Department of Ecology.

Please cite this Chapter as: Print Citation: Bandaragoda, C. , Joanne Greenberg, and Mary Dumas (2013). Data integration of WRIA 1 Hydraulic, Fish Habitat, and Hydrology Models. 134 pp. Nooksack Indian Tribe, Whatcom County, WA. WRIA 1 Joint Board.

Online Citation: Bandaragoda, C. Joanne Greenberg, and Mary Dumas (2013). Data integration of WRIA 1 Hydraulic, Fish Habitat, and Hydrology Models. 134 pp. Nooksack Indian Tribe, Whatcom County, WA. WRIA 1 Joint Board. Retrieved [Date], from http://wria1project.whatcomcounty.org/.

This work was funded by the Nooksack Indian Tribe acting cooperatively as a member of the WRIA 1 Joint Board in support of the WRIA 1 Watershed Management Project; June 2013.


http://wria1project.whatcomcounty.org/

June 2013

DATA INTEGRATION OF WRIA 1 HYDRAULIC, FISH HABITAT, AND HYDROLOGY MODELS TABLE OF CONTENTS

1.0 OVERVIEW ................................................................................................................................... 5

2.0 PURPOSE ....................................................................................................................................... 5

3.0 INFORMATION SUMMARY: WRIA 1 INSTREAM FLOW/FISH HABITAT TECHNICAL WORK PRODUCTS ......................................................................................................... 7

3.1 HISTORY ................................................................................................................................................... 7 3.2 INSTREAM FLOW ................................................................................................................................... 10 3.3 HYDRAULIC MODELS .............................................................................................................................. 11 3.4 HABITAT MAPPING ................................................................................................................................ 13 3.5 HYDROLOGY MODELS ............................................................................................................................ 17 3.6 MANAGEMENT AREA ASSESSMENT SITES ............................................................................................. 19

4.0 ELECTRONIC DATA ................................................................................................................. 23

4.1 DATA INTEGRATION PROJECT DELIVERABLES DISTRIBUTED ONLINE .................................................... 23 4.2 DATA INTEGRATION PROJECT DELIVERABLES ........................................................................................ 24

5.0 REFERENCES .............................................................................................................................. 25 APPENIDX A: SITE INFORMATION…………………………………………………………………………27 COMMENTS……………………………………………………………………………………………………………136


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List of Figures Figure 1. Distribution and types of Assessment sites in WRIA 1. ................................................................. 9 Figure 2. Components of an Ecological Flow Regime (Hardy 2000). ........................................................ 10 Figure 3. Comparison of 2007 (dashed) and 2012 (solid) hydrology model results at Bertrand Creek Intensive Site. .............................................................................................................................................. 18 Figure 4. Bertrand Creek outlet 7Q10 statistic for each month for Existing and Historic Scenarios in the Lower Nooksack Water Budget (Bandaragoda et al. 2012b). Scenario modeled from 06/20/1952-9/30/2011. .................................................................................................................................................. 18 Figure 5. WRIA 1 Management Areas. Full size maps of individual management areas are available at the Introduction to the sites Information organized by Management Area in Appendix A. ...................... 20

List of Tables

Table 1. Data layers for consideration in the stratification of similar river reaches (reformatted from Hardy 2000). .................................................................................................................................................. 8 Table 2. WRIA 1 Fish species and lifestage list. .......................................................................................... 16 Table 3. Assessment sites listed by Management Area (alphabetical order). ........................................... 21


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1.0 OVERVIEW

This work, Data Integration of WRIA 1 Hydraulic, Fish Habitat, and Hydrology Models, is intended to increase the usability of existing data and to help achieve the overall goals of the Water Resources Inventory Area No. 1 (WRIA 1) Watershed Management Project. No new modeling was performed as part of this technical project.

The goal of integrating hydraulic, hydrology and fish habitat models is to describe the relationship between weighted usable area and streamflow for species and life stage utilization throughout the year. The project work consists of a comparison of previous and updated model results (Tarboton 2007, Bandaragoda et al. 2012b), previous instream flow recommendations were constrained at the lower and upper bounds by the 90% and 10% exceedence flows. The updated model results for the 10%, 50%, and 90% exceedence flows are presented, as well as the WUA based fish flows bounded by the 10% and 90%. Additionally, this work is intended to increase the accessibility of technical information from previous work conducted for the WRIA 1 Joint Board.

The project team reviewed and summarized WRIA 1 Decision Support System (DSS) databases related to fish habitat models, hydraulic models, and hydrology models prepared as part of the WRIA 1 Watershed Management Project (Tarboton 2007, Bandaragoda et al. 2012b). We present the probability of exceedence and maximum habitat curves for all intensive and Rapid Assessment sites (37) from the 2005 WRIA 1 Watershed Management Plan calculated for comparison with those calculated using the results from the Lower Nooksack Water Budget (Bandaragoda et al., 2012b) calibration of the WRIA 1 watershed model, Topnet-WM.

Outcomes from this technical work include an integrated database of hydraulic, fish habitat, and hydrology model results as well as site “At-A-Glance” snapshots that display a range of complex and interrelated data in an accessible format for Intensive Sites located in the Bertrand Creek, Tenmile Creek, North Fork, South Fork and Middle Management Areas.

2.0 PURPOSE

The purpose of this work is to increase the usability of existing data for individuals, non-governmental organizations, and government agencies working on watershed management and salmon recovery in WRIA 1.

A majority of this report is based on the work of Thom Hardy and Craig Addley and other contributors at Utah State University (USU) that was completed as part of the WRIA 1 Watershed Management Project (Hardy 2000, Hardy et al. 2002, Hardy 2002f, Hardy 2002a, e, b, Saraeva and Hardy 2006).

Key terms used for describing the existing data and models relied upon to estimate stream flow and fish habitat are summarized on the following page and serve as a glossary for this report, appendices, and technical memos.


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Key terms used for describing the existing data and models relied upon to estimate stream flow and fish habitat include:

‣ Hydraulic Model: A representation of surface water flow in a channel.

‣ Hydrology Model: A representation of the rainfall-runoff process in a drainage system.

‣ Fish Habitat Model: Physical Habitat Simulation Model (PHABSIM)

‣ Water Budget: An analytical tool used to track or account for water movement between components of the hydrologic cycle.

‣ Drainage: An area of land that contributes water, sediment, and dissolved materials to a common outlet; in the WRIA 1 Watershed Management Project; a drainage is the geographic scale of model results used for balancing water movement.

‣ Node: Short for “computational node”, a location along a stream or river channel where hydrologic model output is calculated and reported. For the WRIA 1 Watershed Management Project, computational nodes were located at the downstream outlet of each drainage, at U.S. Geological Survey stream gage locations, and at instream flow quantification sites.

‣ Weighted Usable Area (WUA): An integrated measure of both habitat quantity and quality for specific fish species and life stages as a function of stream flow. The WUA curve gives the flow that maximizes habitat given the hydraulics of the channel and requirements of each species for types of habitat.

‣ Mean Annual Flow (MAF): The average annual flow of a drainage in cubic feet per second (cfs) or as a percentage of the mean annual flow (MAF%) of that would occur under predevelopment conditions (based on Historic Scenario hydrologic modeling).

‣ Exceedence Probability: The chance that a specified flow during a particular month will be exceeded in any given year.

‣ Extrapolating: The process of using measured data and a numerical methodology to develop estimates for locations where measured (observed) data are not available.


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3.0 INFORMATION SUMMARY: WRIA 1 Instream Flow/Fish Habitat Technical Work Products

3.1 History The overall goal of the WRIA 1 Watershed Management Project is to have water of sufficient quantity and quality to meet the needs of current and future human generations. This goal includes the restoration of salmon, steelhead, and trout populations to healthy and harvestable levels, and the improvement of the habitat upon which fish rely. Since the inception of the Project in 1998, steps have been taken to achieve this goal, including the development of the technical information necessary to evaluate instream (see Reference section of this document and described below) and out-of-stream needs determined in the Lower Nooksack Water Budget (Bandaragoda et al. 2012b). The goal of integrating hydraulic, hydrology and fish habitat models is to describe the relationship between weighted usable area and streamflow for species and life stage utilization throughout the year. In 1999, the Instream Flow Methods Conference achieved agreement among the invited experts on the most appropriate method(s) for estimating an accurate relationship between streamflow and fish habitat quantity and quality in Water Resources Inventory Area 1 (WRIA 1) (Freimund 1999). In October 2000, a Habitat Suitability Criteria (HSC) workshop was conducted and the Instream Flow and Fish Habitat technical team members identified by consensus the criteria that would be used in the habitat models for the selected field sites (Hardy 2002d, Hardy 2002e). Over the 2000 through 2004 period, sites where field data were to be collected were identified by consensus of the Instream Flow and Fish Habitat technical team members based on a number of factors including representativeness of the site, the availability of fish utilization data (e.g., spawner surveys, smolt traps), locations where instream flows were established by Ecology in 1985 (WAC 173-501), and management issues or where known conflicts over water use existed. The field data collection and analyses of the collected field data were conducted to implement the agreed upon most appropriate methods for estimating the relation between streamflow and fish habitat quantity and quality at 37 sites within WRIA 1 (Figure 1). After collecting hydraulic and fish habitat characteristics of these locations, Intensive and Rapid Assessment sites were incorporated into the hydrology model node structure used in the first implementation of the WRIA 1 Watershed Modeling using Topnet-WM (Tarboton 2007) as well as the second implementation focused on estimating the Lower Nooksack Water Budget (Bandaragoda et al. 2012b).

In April 2002, the WRIA 1 Watershed Management Project and associated Instream Flow (ISF) and Fish Habitat (FH) Technical Teams sponsored an Extrapolation workshop to investigate how instream flow modeling results from 20 intensive study sites located in WRIA 1 could be used to reliably identify an ecological flow regime at other locations throughout WRIA 1 where field data had not been collected. This workshop was technical in nature and was attended by ISF/FH Technical Team members, Washington State Department of Ecology, and other Project participants. The goal of extrapolating the model results was to provide an estimate of Instream Flow Needs (IFN) for each computational node of the WRIA 1 Watershed Management Project for the purpose of selecting and setting an instream flow regime throughout the WRIA (Hardy 2002a).


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In May 2002, an Instream Flow Selection Methodology Symposium was sponsored by the WRIA 1 Watershed Management Project to provide information on technical, legal, and policy considerations related to selecting and adopting instream flow levels. One of the symposium goals was to help the WRIA 1 Watershed Management Project participants efficiently identify a workable action plan for developing recommendations on an ecological flow regime for locations throughout WRIA 1 that would achieve the Project goals in the context of the multiple demands of out-of-stream water users and federal, state, and tribal laws (Hardy 2002b, c). Following this symposium, an inter-governmental working group was assigned by the WRIA 1 Joint Board to develop an Instream Flow Selection and Adoption Action Plan. This plan was developed and was incorporated as Appendix C in the WRIA 1 Watershed Management Plan – Phase 1 adopted by the Project participants in March 2005. A drainage stratification process was developed to support the extrapolation of the field tested model results to other non-Assessment sites (Saraeva 2006, Saraeva and Hardy 2006, Saraeva 2007). As summarized in Table 1, the stratification procedure identified self-similar drainages based on physical and biological characteristics and location within WRIA 1. The instream flow modeling results from the Intensive and Rapid Assessment sites were associated with the different stratum and then extrapolated to computational nodes at the other drainages within the same stratum. Table 1. Data layers for consideration in the stratification of similar river reaches (reformatted from Hardy 2000).

Category

Data

Lay

er

Basin Characteristics

Species and Life Stages

Vegetation

Hydrology Water Quality

Land Use

Size

Distribution Age Precipitation 303(d) Classification

Permeability

Aspect Channel Form

Timing Composition Relief Point/ Non-Point Loadings

Land Use Classification

Slope Drainage Density

Composition Condition Water Source (e.g., glacial, snow)

Sediment Regime

Elevation Timing Riparian Presence/ Absence

Surficial Geology

Status

Soil Types Barriers Stability Index

Relief Abundance

Valley Type

Basin Shape


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Figure 1. Distribution and types of Assessment sites in WRIA 1.


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3.2 Instream Flow Instream flow preserves, protects, and restores the physical, biological, and chemical aspects of water, and can be divided into five functional categories: 1) water quality maintenance, 2) fisheries baseflow, 3) channel maintenance, 4) riparian maintenance, and 5) valley maintenance, as shown in Figure 2. In early WRIA 1 Watershed Management Project work (Hardy 2000) each of these flow components were identified as essential for maintaining the ecological health of the stream system, although valley maintenance flows were not included as an instream flow requirement as these are generally catastrophic flood property-damaging events. Most quantification methodologies currently recognize that suitable flow regimes can be broken down into the first four basic flow components (Hill et al. 1991, Petts et al. 1995).

Figure 2. Components of an Ecological Flow Regime (Hardy 2000).

Valley maintenance flows (Figure 2) are infrequent very large flood events (500-yr floods) and are generally associated with catastrophic loss. Riparian maintenance flows (Figure 2) are needed to maintain stream corridor vegetation and habitat. Channel maintenance flows (Figure 2) are important for generating channel characteristics such as riffles, runs, and pools in sufficient quantity and quality to support aquatic habitat. Fisheries baseflow (Figure 2) is the minimum instream flow needed to support fish populations during various life stages. A Washington State rule was established in 1985 (WAC 173-501) for instream flows in WRIA 1. Water quality maintenance flows (Figure 2) are the lowest quantity of streamflow necessary to assimilate wastewater and comply with water quality standards.

The four major components of a stream system that determine productivity for aquatic organisms are:

‣ (1) flow regime,

‣ (2) physical habitat structure (e.g., channel form and substrate distribution),

‣ (3) water quality (e.g., temperature, dissolved oxygen), and

‣ (4) energy inputs from the watershed (e.g., nutrients and organic matter).


June 2013

In river systems, the suitability of environmental conditions for aquatic resources is directly related to the characteristics of the flow regime. Therefore, quantification of a flow regime which will provide long-term protection of the aquatic resources should identify the environmental conditions that operate to limit aquatic species, as well as identify a flow regime that will ensure the formation and persistence of key environmental conditions (Hardy 2000).

3.3 Hydraulic Models In general, hydraulic modeling associated with quantifying a relation between flow and fish habitat quantity and quality occurs on a limited longitudinal extent of a study reach with downstream and upstream hydraulic controls selected to be a representative area. At each hydraulic control point, a cross section which is perpendicular to the axis of the river flow was permanently marked on both sides of the riverbank. The position of these markers (i.e., head pins) was established at an elevation clearly in the upland vegetation zone. These head pins were used as the survey elevation control to mark the upper and lower bounds of the study segment. Continuous temperature data probes were also established at each intensive site to allow for potential temperature modeling at the sites. The delineation of the channel topography and related hydraulic properties were dictated by the size and characteristics of the stream or river segment being studied and whether or not a site was an “intensive” site modeled using the two dimensional (2-D) variation of the Physical Habitat Simulation Model (PHABSIM) or the one-dimensional (1-D) variation of PHABSIM. These distinct technical steps are summarized in the following three sections, with technical tasks conducted in this project summarized by segment characteristics. The following descriptions of previous work are summarized from a Technical Evaluation of 2000 Field Season (Hardy 2002d).

Field Data Collection

The objective of this task (Instream Flow Incremental Methodology Task 2.3.2) was to collect the field data needed to apply the computer models identified during the instream flow methods selection workshop (Hardy 2002a). Field data collection at the selected sites included establishing control point networks, conducting longitudinal profile surveys, measuring channel topography and hydraulic properties, characterizing the channel substrate, identifying riparian vegetation and the horizontal extent of the riparian zone, mapping fish habitat, and mapping large woody debris (Hardy 2002d). Longitudinal Profile Survey After establishing survey control network at both the small stream and large river study sites, a longitudinal survey of water surface elevations (WSEL) was initiated. At the beginning of the longitudinal profile survey, an up- and downstream water surface elevation was recorded and a discharge measurement was collected so that the longitudinal profile survey could be used to calibrate hydraulic models to an observed flow with known boundary conditions. The WSEL surveys began in late July 2000 when flows at the sites were at or approaching base flow values.


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Collection of Channel Topography and Hydraulic Properties At all the small stream sites conventional one-dimensional (1D) cross section data were collected using survey equipment, velocity meters (Marsh-McBurney), and fiberglass tapes pulled across the channel and anchored to the headpins. At each cross section the out of channel and in channel geometry was measured at horizontal increments that ensured the topographical variation along the cross section was collected. In addition to collecting a distance and elevation, velocity measurements were recorded for the instream section of the survey. On Tenmile, Anderson, North Fork Dakota, Whatcom, and Fishtrap Creeks two- and three dimensional (2/3D) data were collected in addition to the 1D data so that multi dimensional modeling of these sites can be conducted. These multi-dimensional data were collected using a Vulcan system. Instream mapping and stream velocity data acquisition was accomplished on the large river sites using GPS, single beam sonar, and Acoustic Doppler Current Profiler (ADCP) sonar equipment (hydroacoustic) mounted on a cataraft boat. Out of the wetted channel topography and shallow water zones were mapped based on low elevation, high-resolution aerial photographs of the study reaches. The data collected by the hydroacoustic equipment are coupled with the time and location data from the GPS and the computers logging the depth and velocity data. The hydroacoustic based mapping of the subsurface channel topography (i.e., under water topography) was collected with a minimum target spatial sampling density of 0.5-2.5 feet. It was also augmented with finer detail data where channel complexity is high. Greater or lesser target spatial resolutions may be dictated by the relative complexity in channel topographies. Hydroacoustic mapping was conducted at a discharge greater than the discharge at which the aerial photogrammetry was collected to ensure an overlap between these data sets and to minimize the potential for missing topographies where the acoustic mapping was limited by water depths at the stream margins. The integration of photogrammetry and hydro-acoustic data task incorporated the three-dimensional terrain data derived from the softcopy photogrammetry and the three-dimensional terrain data derived from the hydro-acoustic data. This task generated a single spatially explicit terrain model for each intensive study site.

Model Development

The techniques used to simulate hydraulic conditions in a stream can have a significant impact on habitat versus stream flow relationships determined in the habitat modeling (e.g., PHABSIM). The correct choice of hydraulic models as well as proper calibration often represents the most difficult step in the process of analyzing instream flows. The assumption that the shape of the channel does not substantially change with streamflow over the range of flows being simulated. The first step in hydraulic modeling within PHABSIM is the calibration and simulation of water surface elevations. In the case of reliance on 1-dimensional hydraulic simulations of water surface elevations and velocities (e.g., PHABSIM), model validation should be approached from several perspectives. In terms of water surface elevations, the difference between observed and simulated water surface elevations at the calibration flows was the primary criteria (e.g., +/- 0.05 feet).


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Two- and 3-dimensional flow models require various boundary conditions such as the beginning downstream water surface elevations, discharge, accurate 3-dimensional channel topography, and spatially distributed substrate or roughness. In addition, accurate results require calibration and validation data in the form of longitudinal water surface profiles and measured velocities. The hydraulic model calibration task involved a two-step process. The first step entailed the initial development of the stage-discharge relationships at the upstream end of the reach and at each of the downstream control points at each intensive study site. Once the hydraulic model was calibrated, the measured velocity distributions collected with the acoustic doppler profiler and/or velocity meter were compared to the modeled velocity distributions at each calibration discharge. This step was used to assess the quality of the hydraulic modeling. Due to the time and budgetary constraints, hyporheic zone determinations were not completed, however, the importance of the hyporheic zone (i.e., areas of ground water infiltration within the channel) in rivers to spawning salmonids in terms of redd locations or for use as thermal refugia is well documented.

3.4 Habitat Mapping The site-specific habitat mapping focused on the acquisition of ground based habitat delineations using a standardized classification system to determine the type, distribution, and amount of specific habitat types within the river reach. Each habitat type was delineated in terms of its length and average width. In those instances where selected river systems are of moderate to large scale (i.e., average widths greater than approximately 50 feet), the habitat typing was accomplished through the use of high resolution aerial photographs collected specifically for the project. For smaller systems the habitat mapping was accomplished by ground based surveys. This was accomplished with the use of hip chain, laser range finder, survey tape, or GPS. Habitat types were broken into the basic types that included runs, pools, riffle and glides (glides are shallow runs typically containing larger substrate characteristics). Other features such as backwater zones were noted and qualifying descriptions of the reaches were made during the mapping process.

Substrate Characterization

Substrate mapping for both the exposed and submerged portions of the study sites was accomplished by a variety of approaches including: observation made from the shore, wading, or from the boat; by snorkeling sections of the river; and by using a submergible video camera. As part of the 1D data collection effort at the small stream sites, substrate data were collected along the cross section transects.


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Riparian Zone Characterization

The riparian zone characterization was performed to determine the riparian species composition, the elevation range within the riparian zone, and the lateral extent of the riparian zone from the channels at both the large and small study sites. On the small stream sites, the riparian zone characterization was performed at the upstream, middle, and downstream cross sections that were previously established at each site. The characterization was accomplished by measuring the distance from the start of the riparian zone at the edge of water along the transects away from the channel to the transition zone of upland vegetation. For the large river sites the same quantification was completed but the method used was different. The transitional locations between the riparian vegetation types were marked on the high-resolution aerial photographs. It was determined that this method was a much more efficient approach than the one used on the small streams.

Habitat Mapping

The meso-habitat types within the small stream reach segments were mapped from the downstream to upstream boundaries. Habitat types were broken into the basic types that included runs, pools, riffle and glides (glides are shallow runs typically containing larger substrate characteristics). The meso-habitat at the larger river sites was mapped using a combination of walking and boating along the channel. The length of the river that was mapped for each site was a function of the geomorphic characteristic of the site and how far this characteristic extended above and below the site boundaries. Large woody debris was qualitatively identified and geo referenced to cross section locations at the small stream sites. On the small stream sites that were mapped using the 2/3D equipment, individual pieces were mapped. For the large river sites it was determined that large woody debris would be mapped using the high-resolution aerial photographs.

Characterization of the Invertebrate Community

The characterization of the invertebrate community task entailed the collection of three replicate drift samples below a riffle for each selected stream reach. If possible, three replicate drift samples were taken from three separate locations corresponding to the left, center, and right sides of the stream channel. Aside from the importance of characterizing the invertebrate community of the aquatic resources at each site, one of the proposed modeling approaches involved the application of an individually mechanistic based bioenergetic model for salmonids. In order to apply this model, the hydraulic model output was integrated with both temperature and food availability. The food availability was determined from an estimate of the drift density and size characteristics. The fish species and life stage habitat utilization task focused on the verification of fish species and life stage within each study reach in a manner that maximized the potential for validation of both physical habitat and bioenergetic (or other) modeling. Each habitat type available within a study reach was sampled using equipment types and sampling strategies appropriate for each target species and life stages.


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Habitat Suitability Curves

Due to the prohibitive time and cost constraints associated with attempting to develop site specific habitat suitability curves (HSC) for each stream reach across all potential strata, interim HSC were selected. Available HSC for all target species and life stages were assembled from the literature for consideration for use within WRIA 1. In October 2000, a Habitat Suitability Criteria (HSC) workshop was conducted and the ISF/FH Technical Team members identified by consensus the criteria that would be used in the habitat models for the selected field sites (Hardy 2002d, Hardy 2002e). The validation of the interim HSC was contingent on the available biological field data for specific species, life stages, and season. Due to the time and budgetary constraints associated with the Project, HSC specific to the Nooksack River system were not developed.

Habitat Model Development

The physical habitat modeling was approached differently depending on the specific life stages considered for different species. For example, spawning analyses only included habitat units that species were known to utilize for spawning, including depth, velocity, and substrate and relied on the integration of the hyporheic analyses described previously. Analysis of fry and juvenile habitats incorporated restrictions in the simulations that evaluate distance from the shoreline or presence of cover to reflect the known behavioral dependences to these factors in salmonids. Spatially explicit maps of simulated fish habitat quantity and quality for each species and life stage based on HSC criteria were generated at each site for all modeled flows. In addition, these spatially explicit maps included individual and combined suitability factors to aid in the validation of the HSC. The basic habitat versus discharge relationship represents an aggregation of the component cell Weighted Usable Area (WUA) values across all cells at a specific discharge for a given species and life stage. Computational techniques were available that permit the user to determine the component areas associated with given thresholds of combined suitability. The peak of the total habitat curve does not always correspond with the peak of highly suitable habitat conditions. Because species and life stages vary in habitat preferences, WUA curves maximized at different flows for different species and life stages. The species and life stages in WRIA 1 are listed in Table 2. The WUA curve gives the flow that maximizes habitat given the hydraulics of the channel and requirements of each species for types of habitat. The WUA curve can be bounded by the 10% and 90% exceedence probability to fit the habitat requirements within the hydrology model simulations. According to Beecher (2004), flows should last at least 3-7 days to have a strong biological benefit, although shorter freshets also have biological benefits. A flow that lasts at least 3-7 days would allow a period of sustained rearing with growth and fitness benefits to the fish. Because severe impacts to a population propagate through several generations and can be tracked in run sizes (particularly Pink and Coho salmon, which tend to all be the same age in a year), benefits should also propagate through several generations.


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Table 2. WRIA 1 Fish species and lifestage list. Species Life Stage

Chinook

Spawn Stream Spawn River Spawn Large River Holding Juvenile Fry

Fall Chum Spawning

Coho

Spawning Juvenile Fry

Pink Spawning Sockeye Spawning

Rainbow Trout Spawning Juvenile to Adult Winter

Trout and Steelhead Fry

Steelhead Spawning Juvenile

Cutthroat Spawning Juvenile to Adult

Native Char Spawning Juvenile to Adult

Kokanee Spawning

Mountain Whitefish Juvenile Adult


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3.5 Hydrology Models The balance between supply and demand for water in a river basin can be complicated, and may vary significantly both within and between years due to varying climate conditions and rates of use. Human activities can significantly alter the water balance of drainages, having potential effects on stream ecosystems through changes in both water quantity (habitat availability) and water quality (nutrients, temperature). Simulation modeling is one way of quantifying the likely implications of proposed water management regimes in such complex settings. The more hydrologic data that can be collected, the more accurate the resulting estimates of the five flow components identified as essential for maintaining the ecological health of the stream system. When and where hydrologic data are not available, a simulation model is useful for representing the watershed system. In 2007, the Topnet-WM model was applied in WRIA 1 (Tarboton 2007). Topnet-WM is a distributed hydrologic model with topographically delineated drainages that discharge water into the stream network and are subsequently route the water to the outlet. Topnet-WM includes the integration of rainfall-runoff, snowmelt and evaporation processes, as well as water management activities such as irrigation, artificial drainage, impervious areas, out-of-stream demands and instream flow requirements. These new features were specifically added to address the water resource management issues in the Nooksack River basin in WRIA 1 where potential and actual competition for water resources exists among water users, and between consumptive uses and instream environmental requirements. Due to the dynamic nature of data availability, climate, land use, and decision-making processes, watershed models often need to be updated in order to maintain usefulness and accessibility for users. In 2012, the Lower Nooksack Water Budget project updated the Topnet-WM model for climate and land and water use data inputs across WRIA 1 in the Lower Nooksack. For a general comparison of monthly average results, Figure 3 shows the 2007 results (dashed) compared to the 2012 results (solid) compared to the 2012 hydrology results (10% exceedence flows) for the Bertrand Creek intensive site. For an in depth comparison of the model results between 2007 and 2012 modeling, see Chapter 10 Model Calibration of the Lower Nooksack Water Budget (Bandaragoda 2012). In Figure 3, the statistics represent a monthly average for 10%, 50% and 90% of flows. In Figure 4, the 7Q10 statistic is shown for Bertrand Creek to illustrate the difference between the discharge below which the annual 7-day minimum flow falls in 1 year out of 10 (or 10% 7 day minimum rather than 30 day or monthly average as shown in Figure 3).


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Figure 3. Comparison of 2007 (dashed) and 2012 (solid) hydrology model results at Bertrand Creek Intensive Site.

Figure 4. Bertrand Creek outlet 7Q10 statistic for each month for Existing and Historic Scenarios in the Lower Nooksack Water Budget (Bandaragoda et al. 2012b). Scenario modeled from 06/20/1952-9/30/2011.

0

20

40

60

80

100

120

140

160

180

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

Disc

harg

e (c

fs)

10% Exceedence Flow 200750% Exceedence Flow 200790% Exceedence Flow 200710% Exceedence Flow 201250% Exceedence Flow 201290% Exceedence Flow 2012100% Max Habitat


0

10

20

30

40

50

60

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

Mon

thly

7Q

10 (c

fs)

Existing Historic (~200 years ago)

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The 2012 data update and calibration (Bandaragoda 2012) improved previous model results, especially improving the fit to the daily hydrograph during low flows, but not necessarily on an monthly average. The process of model calibration is complex because of limitations in models, input and output data, mathematical structure of the models, quantitative methods used to fit the model to the data, and imperfect knowledge of basin characteristics (Schaake 2003). The calibration approach applied to develop the Lower Nooksack Water Budget (Bandaragoda 2012) used an aggregate statistic over four years of daily time series data to determine which parameters provide the “best fit” between modeled and observed streamflow data. There is a degree of uncertainty in the calibration process where the modeled streamflow ‘bounds’ the observed streamflow. The degree of uncertainty in the streamflow data used to fit the model is published with each daily data value (observed streamflow ratings and data quality qualifiers available in the updated streamflow database, described in Chapter 10 Streamflow (Bandaragoda et al. 2012a). The degree of uncertainty in the climate data at each drainage and model representation of physical processes for each drainage cannot be known without additional measurements. On an annual basis, the 2012 model trend is lower than the observed streamflow. On a daily basis, some streamflow events are a good fit and others are not. Generally, the low flows are a better fit than the high flows and 2012 model results are an improvement to the 2007 model, this can be determined statistically (see Bandaragoda (2012);Table 3) as well as visually from daily hydrographs (Bandaragoda (2012); Figure 14, Figure 15, Figure 16).

3.6 Management Area Assessment Sites This section is an orientation to the Management Areas and Assessment Sites listed in Appendix A: Drainage Information from Data Integration of WRIA 1 hydraulic, fish habitat and hydrology models. Maps are provided for each Management Area shown in Figure 5 giving locations of the fish habitat, hydraulic and Topnet-WM model Assessment site information. For each Management Area, data tables and figures are provided for each of the 37 Intensive and Rapid Assessment sites and include the following technical information on conditions: 2012 10%, 50%, and 90% exceedence flows, fish habitat information, priority fish species, and life stage graphs. In Table 3 all 37 sites are listed, however, Assessment sites do not always correspond with stream gage locations. Stream gages were installed, in some cases, to comply with the 1985 IRPP and some assessment sites were selected at more representative locations of ideal habitat. For the Bertrand Creek, Tenmile, Middle Fork, South Fork and North Fork watersheds, the points (nodes) with data observations and drainage outlets are listed for easy reference, including stream gages and the drainage outlet. The Management Areas and corresponding sites by drainage are listed in alphabetical order.


June 2013

Figure 5. WRIA 1 Management Areas. Full size maps of individual management areas are available at the Introduction to the sites Information organized by Management Area in Appendix A.


June 2013

Table 3. Assessment sites listed by Management Area (alphabetical order).

Management Area Drainage Name Station Name MAF (cfs) Site Type

Bellingham Bay Chuckanut Chuckanut Creek 8 Drainage Outlet

Bellingham Bay Lower Squalicum Squalicum Creek Upper & Lower Intensive Site 12 USU Intensive Site

Bellingham Bay Whatcom Whatcom Creek Intensive Site 123

USU Intensive Site

Drayton Harbor Haynie Haynie Rapid Assessment Site 3

USU Rapid Assessment Site

Drayton Harbor North Fork Dakota Dakota Creek Intensive Site 8

USU Intensive Site

Lake Whatcom Austin/Beaver Austin Creek Upper & Lower Intensive Site 12

USU Intensive Site

Lower Mainstem Nooksack

Nooksack Channel (water)

Nooksack River at Lynden Intensive Site 3452

Point of withdrawal for water

Lower Mainstem Nooksack Tenmile Tenmile Creek Intensive Site 20

USU Intensive Site

Lynden North Bertrand Bertrand Creek Intensive Site 34 USU Intensive Site

Lynden North Fishtrap Fishtrap Creek Intensive Site 35 USU Intensive Site

Lynden North Kamm Kamm Rapid Assessment Site 1 USU Rapid Assessment Site

Middle Fork Nooksack Lower Middle Fork Nooksack

Middle Fork Nooksack Intensive Site 541

USU Intensive Site

Middle Fork Nooksack Porter Porter Creek 20 DOE ISF Site

Middle Fork Nooksack Sister Sister Creek Upper & Lower Rapid Assessment 26


North Fork Nooksack Canyon Lake Canyon Lake Rapid Assessment Site 41 Streamflow Gage

North Fork Nooksack Coal Coal Creek near Kendall Rapid Assessment 16 Streamflow Gage

North Fork Nooksack Cornell Cornell Creek 21 DOE ISF Site North Fork Nooksack Hendrick Hendrick Creek 8 Drainage Outlet

North Fork Nooksack Kendall Kendall Creek at mouth, at Kendall 98 Streamflow Gage

North Fork Nooksack Kenny Kenney Creek 9 Drainage Outlet

North Fork Nooksack Lower Ruth Lower Ruth Creek Rapid Assessment Site 102


North Fork Nooksack Maple Maple Creek Intensive Site 50 USU Intensive Site

North Fork Nooksack Racehorse Racehorse Creek at North Fork Road 46 Streamflow Gage

North Fork Nooksack Slide Mountain North Fork Nooksack Intensive Site 1389

USU Intensive Site


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Management Area Drainage Name Station Name MAF (cfs) Site Type

Silver/Nooksack Channel & Delta

Nooksack Channel (water) Ferndale Intensive Site 3646

USU Intensive Site

Silver/Nooksack Channel & Delta

Nooksack River Delta Nooksack River at Estuary 3652 Drainage Outlet

South Fork Nooksack Bell Bell Creek Rapid Assessment Site 40


South Fork Nooksack Deer, Roaring, & Plumbago

Deer Creek Rapid Assessment Site 4


South Fork Nooksack Hutchinson Hutchinson Creek 83 DOE ISF Site

South Fork Nooksack Lower South Fork Nooksack South Fork Lower 1109 Drainage Outlet

South Fork Nooksack South Acme Area South Fork Upper 946 Drainage Outlet

Sumas River Breckenridge Breckenridge A 10 USU Rapid Assessment Site

Upper Mainstem Nooksack Lower Anderson

Anderson Creek Upper & Lower Intensive Site 16

USU Intensive Site

Upper Mainstem Nooksack

Nooksack Deming to Everson Nooksack River at Everson 3452 Drainage Outlet

Upper Mainstem Nooksack

Nooksack Deming to Everson

Nooksack River at Deming Confluence Intensive 3364 Mixing Node

Upper Mainstem Nooksack Smith Smith Creek 30 DOE ISF Site


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4.0 ELECTRONIC DATA

Electronic Data Tables structure the organization of the Lower Nooksack Water Budget Project deliverables including those containing source data, code and other intermediary data products to be published on the WRIA 1 Watershed Management Project website (hyperlink here).

4.1 Data Integration Project Deliverables Distributed Online Electronic Data Table 1. Structure for data organization to be used for online publication. Description Folder & File Name(s)

Project report WRIA 1 Data Integration_2013.pdf Appendix A Comments WRIA 1 Data Integration_2013.pdf

Electronic Data Table 2. Structure for ArcGIS Geodatabase < WRIA1DataIntegration2013.gdb>. Description Folder & File Name(s)

WRIA 1 nodes (337) with complete labeling and MAF. GIS Shapefile. Provided by Lummi Nation and updated. wria1_337_nodes.shp Intensive & Rapid Assessment Sites (37) AssessmentSites_37.shp

WRIA 1 geography files

WRIA 1 boundary.shp Bsnwria1_v7_Subbasin.shp WRIA1 management areas.shp TopnetWMStreamNetwork.shp

Sites used in Instream Resources Protection Program (Washington State Department of Ecology 1985) IRPP Sites. Provided by Dept. of Ecology IRPP Sites.shp


http://wria1project.whatcomcounty.org/

June 2013

4.2 Data Integration Project Deliverables

Electronic Appendix Table 2 gives the structure for data organization for the electronic appendix of source and intermediate and final products generated during the technical development and review cycles.

Electronic Data Table 2. Archived data. Folder Name Folder & File Name(s)

Instream Fish Flow Habitat/Methods

Methods Folder (13 files): Symposium and meeting reports, Hal Beecher explanation of bounding flows, extrapolation techniques.

Instream Fish Flow Habitat/Periodicity & Prioritization

DecisionMemo2004 on priority species.doc Fish_Periodicity_Tables_2003.xls Fishdistributionperiodicity_2001.pdf (Anchor Report)

Instream Fish Flow Habitat /Results Results (12 files) with spreadsheets and graphs of WUA curves and habitat graphs

Instream Fish Flow Habitat/ documents

IRPPflows.pdf ISF and FH Overview013106.pdf ISFandFH_Technical_Team_Members_List.pdf Selected 2000 Instream Flow Study Locations.pdf WhatcomCountyHydroMapWithAssessmentSites20110616.pdf

WUA documentation WUA Documentation folder (22 files) FINAL Weighted Usability Area Curves (WUAs) Output tables and graphs (75 files)

Hydraulic Modeling

Intensive_Sites_Hydraulic_Modeling_web.pdf Intensive_Sites_Hydraulic_Modeling_document.pdf FieldWorkTask7SummaryReportFinal.pdf

Hydrology ExceedenceTables2007 Exceedence tables for 337 nodes and four scenarios (4 files)

Hydrology ExceedenceTables2012

Two folders for existing and historic scenarios. Exceedence tables (xls), full modeled flow output (txt), Matlab code

Documents/Appendix Development Folder of spreadsheets used for developing charts and tables in Appendix A (12 files)

Documents/EndnoteCitations Endnote Database with electronic links to available documents.

Documents/Figures Figures used in this report

WRIA 1 DSS/Technical Documentation

Habitat time series analyst, macroinvertebrates, 1D and 2D Instream Flow table and data field details

WRIA1DSS/GIS Data/Shapefiles 42 shapefiles related to WRIA 1 geography and USU data collected

WRA1DSS/DSS_Data (12G) 2D Data, Macroinvert Data, PhabSim Data, Well log Data, Photos


June 2013

5.0 REFERENCES Bandaragoda, C. 2012. Model Calibration. Pages pp. 317-344 in C. Bandaragoda, J. Greenberg, M. Dumas, and P. Gill, editors. Lower Nooksack Water Budget. WRIA 1 Joint Board, Whatcom County, WA.

Bandaragoda, C., L. Doremus, and J. Greenberg. 2012a. Streamflow Observed Data. Pages pp. 288-316 in C. Bandaragoda, J. Greenberg, M. Dumas, and P. Gill, editors. Lower Nooksack Water Budget. WRIA 1 Joint Board, Whatcom County, WA.

Bandaragoda, C., J. Greenberg, D. M., and P. Gill. 2012b. Lower Nooksack Water Budget Overview.in C. Bandaragoda, J. Greenberg, D. M., and P. Gill, editors. Lower Nooksack Water Budget. WRIA 1 Joint Board, Whatcom County, WA.

Beecher, H. 2004. 10% Exceedence flow as cap for instream flows.

Freimund, J. 1999. Staff Report on Instream Flow Methods Conference.

Hardy, McKee, Kaluarachchi, Kemblowski, Tarboton, Stenes, and Pack. 2002. WRIA I Watershed Management Project Phase II Technical Study Results: Executive Summary. Utah Water Research Laboratory, Utah State University.

Hardy, T. B. 2000. A Conceptual Framework and Technical Approach for Assessing Instream Flow Needs in the Water Resources Inventory Area No. 1 (WRIA 1) in Washington State. Utah State University, Logan, Utah.

Hardy, T. B. 2002a. Instream flow extrapolation workshop: Draft Summary Staff Team Report. Utah Water Research Laboratory, Logan, Utah.

Hardy, T. B. 2002b. Instream Flow Selection Methodology Symposium - Summary Report. Utah State University.

Hardy, T. B. 2002c. Instream Flow Selection Methodology Symposium Proceedings.in WRIA 1 Watershed Management Project, Bellingham, WA.

Hardy, T. B. 2002d. Technical Evaluatio of FY 2000 Field Season.

Hardy, T. B. 2002e. WRIA 1 Habitat Suitability Criteria Workshop. Utah Water Research Laboratory, Logan, Utah.

Hardy, T. B. 2002f. WRIA 1 Habitat Suitability Criteria Workshop Summary Report.

Hill, M. R., W. S. Platts, and R. L. Beschta. 1991. Ecological and geomorphological concepts for instream and out-of-channel flow requirements. Rivers 2:198-210.

Petts, G., I. Maddock, M. Bickerton, and A. J. D. Ferguson, editors. 1995. Linking hydrology and ecology: The scientific basis for river basin management. In: The ecological basis for river management. . John Wiley and Sons, West Susex, Engand.

Saraeva, E. 2006. Development of an instream flow based extrapolation procedure for the Nooksack Watershed. Utah State University, Logan, Utah.

Saraeva, E. 2007. Development of an Instream Flow-Based Extrapolation Procedure for the Nooksack Watershed. Utah Water Research Laboratory, Logan, Utah.


June 2013

Saraeva, E., and T. B. Hardy. 2006. Basin Stratification for Use in Extrapolation of Instream Flow Requirements in Watershed Planning. Utah State University.

Schaake, J. 2003. Introduction.in Q. Duan, H. V. Gupta, S. Sorooshian, A. N. Rousseau, and R. Turcotte, editors. Calibration of Watershed Models. American Geophysical Union, Washington D.C.

Tarboton, D. G. 2007. Water Quantity Model Development and Calibration, WRIA 1 Watershed Management Project Phase III, Task 4.1 report. Utah State University, Logan, Utah.

Washington State Department of Ecology. 1985. Nooksack Water Resource Inventory Area Instream Resources Protection Program including Administrative Rules (Water Resource Inventory Area #1). Olympia, WA.
