Overview of the Instream Flow/Fish Habitat Element of the WRIA 1 Watershed Management Project. By Jeremy Freimund, P.H.

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Overview of the Instream Flow/Fish Habitat Element of the WRIA 1 Watershed Management Project By Jeremy Freimund, P.H. January 31, 2006 1

Presentation Outline General Overview Instream Flow and Fish Habitat (ISF/FH) Technical Teams Goals of ISF/FH Element of Project Why are we doing ISF/FH Element How Work Was Conducted Details of Applied Methods and Work Products Modeling Process and Results Species and Life Stage Prioritization Decision Support Information Stratification/Extrapolation Schedule/Next Steps Summary 2

General Overview 3

ISF/FH Technical Teams ISF Tech. Team Lead: Jeremy Freimund (LIBC) Fish Habitat Technical Team Co-Leads: Chris Fairbanks (PUD No. 1) John Thompson (Whatcom County) Important other contributors/participants include: Lummi Nation, Nooksack Tribe, WDFW, Ecology, Whatcom County, Utah State University, PUD No. 1, Bellingham, Diking and Drainage Caucus, Anvil Corporation 4

Goals of ISF/FH Element of Project Accurately estimate the relationship between stream flow and fish habitat quantity and quality for different fish species and life stages in WRIA 1. Integrate results with results from water quantity and water quality elements of project and support salmon recovery efforts. 5

Why are we doing ISF/FH Element To enable knowledge-based decision making based on the best available science Instream flow needs inextricably linked to water quantity and water quality To take action in response to ESA listing To address tribal water right claims To help determine the amount of water available for in- and out-of-stream uses 6

How Work Was Conducted Three Step Technical Process: 1. Identification of the methods to be used (best available science) to estimate the relationship between stream flow and fish habitat quantity and quality 2. Application of selected methods 3. Recommend initial ecological flow regime Selection and Adoption Phase Instream Flow Selection and Adoption Action Plan 7

Step 1. Identify Methods WRIA 1 Watershed Management Project Instream Flow Methods Conference September 15-17, 1999 Local, Regional, National, and International experts participated in the conference Peer-reviewed report issued on conference results March 2000 Concept of Ecological Flow Regime 8

Step 1. Ecological Flow Regime Channel Maintenance Flow Valley Maintenance Flow Riparian Maintenance Flow Fisheries Baseflow Water Quality Maintenance Flow 9

Step 2. Application of Selected Methods Utah State University (USU) selected to implement agreed to methods (Thom Hardy and Craig Addley) Field data collected at 13 intensive study sites in 2000 Field data collected at 9 intensive and 5 rapid assessment sites during 2001 Field data initially collected at a total of 27 sites Habitat Suitability Criteria (HSC) Workshop held Oct. 10-12, 2000 Modeling/analysis of field data initiated during summer of 2001 10

Step 2. Study Site Locations Study sites were identified by consensus of ISF/FH Technical Team members Sites selected based on factors including: Representativeness of site Availability of fish utilization data (e.g., spawner surveys, smolt traps) Ecology overlap sites (n = 16) Management issues overlay 11

Step 2. Study Site Locations 12

Step 2. Extrapolation Extrapolation workshop from April 2-3, 2002 Identify approach to extrapolate relationships between stream flow and fish habitat quantity and quality to downstream end of each drainage in WRIA 1. Approach based on stratification of the 172 drainages in WRIA 1 into self-similar clusters. Field data collected at 14 sites during 2003 and 2004 to validate extrapolation methods. Field data collected at a total of 41 sites (27 initial sites and 14 validation sites) 13

Step 3. Instream Flow Selection Instream Flow Selection Methodology Symposium May 29-30, 2002 (technical, legal, policy experts) In July 2002, the Joint Board established an Intergovernmental Instream Flow Working Group to develop a draft Instream Flow Selection and Adoption Action Plan. June 2005, Instream Flow Selection and Adoption Action Plan adopted as part of the WRIA 1 Watershed Management Plan Version 1. Selection and Adoption Action Plan has two pilot watersheds: Middle Fork Nooksack and Bertrand Creek 14

Details of Applied Methods and Work Products 15

Overview of Instream Flow Technical Element Data Collection Data Analysis Computer Modeling Decision Support Information Hydraulic Data and Channel Structure Representation (i.e., Computational Mesh) Stage-Discharge Relation Stage (m) 106.4 106.2 106.0 105.8 105.6 105.4 0 20 40 60 Discharge (cms) 14000 Available Habitat Versus Streamflow 12000 Method Selection Site Selection Field Data Collection Literature Review Suitability Index Habitat Suitability Criteria Juvenile Chinook 1 0.8 0.6 0.4 Model Calibration Weighted Usable Area (m 2 ) 10000 8000 6000 4000 2000 0.2 0 0 5 10 15 20 25 30 35 40 45 0 0 0.5 1 1.5 2 2.5 3 3.5 4 Flow (cms) 1 Velocity (ft/sec) Juvenile Chinook Utah State University Scientists WRIA 1 Instream Flow and Fish Habitat Technical Teams 0.8 Suitability Index 0.6 0.4 0.2 0 0 1 2 3 4 5 6 Depth (ft) Juvenile Chinook 1 0.8 Suitability Index 0.6 0.4 0.2 16 0 0 10 20 30 40 50 60 70 80 90 100 Cover/Substrate Code

30000 Nooksack River, South Fork Upper All Modeled Species and Life Stages Depth, Velocity, and Substrate Chin_Holding 25000 Chin_Juv Chin_Spawn_LR Chin_Spawn_R Chin_Spawn_S 20000 Chum_Spawn_Fall Chum_Spawn_Sum Coho_Juv WUA (m 2 ) 15000 Coho_Spawn P ink_spawn Sockeye_Spawn B ull_s pa wn Rain_Juv_Ad_Winter 10000 Rain_Spawn Rain_Juv_Ad Steelhead_Spawn Steelhead_Spawn 5000 Trout_Steelhead_Fry Chin_Fry Chin_Fry_Gen Coho_Fry 0 0 5 10 15 20 25 30 35 40 45 Flow (cms) 17

Middle Fork Nooksack - All Modeled Adult (Depth, Velocity and Substrate) Chinook Holding Rainbow Adult Cutthroat Adult Native char Adult Rainbow Winter Mountain whitefish Adult 50000 45000 40000 35000 WUA (square feet/1000 feet) 30000 25000 20000 15000 10000 5000 0 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 Flow (cfs) 18

Middle Fork Nooksack - All Modeled Adult (Depth, Velocity and Substrate) Chinook Holding Rainbow Adult Rainbow Winter Cutthroat Adult Native char Adult Mountain whitefish Adult 100 90 80 70 Percent of Maximum Habitat 60 50 40 30 20 10 0 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 Flow (cfs) 19

Middle Fork Nooksack Chinook Salmon Chinook Spawn Stream Chinook Spawn River Chinook Spawn Large River Chinook Fry Chinook Holding Chinook Juvenile 80000 70000 60000 WUA (square feet/1000 feet) 50000 40000 30000 20000 10000 0 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 Flow (cfs) 20

Middle Fork Nooksack Chinook Salmon Chinook Spawn Stream Chinook Spawn River Chinook Spawn Large River Chinook Fry Chinook Holding Chinook Juvenile 100 90 80 70 Percent of Maximum Habitat 60 50 40 30 20 10 0 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 100 Flow (cfs) 21

Table 1. Recommended rules for determination of priority species/lifestages in the lower and upper watersheds. Geographic Subarea Species Present Priority Species/Lifestages Months Lower Watersheds (downstream of the confluence of the North and South forks of the Nooksack River near Deming, coastal streams including Whatcom Creek, and Sumas River drainage) If chinook, chum, coho, steelhead present, then: If chinook, coho, steelhead present (no chum), then: If coho, chum, steelhead present (no chinook), then: Chinook spawning Fall Chum spawning in current known distribution, otherwise coho spawning Steelhead spawning Steelhead incubation (2/3 of spawning flow) (consider also steelhead juvenile rearing) Chinook spawning Coho spawning Steelhead spawning Steelhead incubation (2/3 of spawning flow) (consider also steelhead juvenile rearing) Steelhead incubation (2/3 of spawning flow) (consider also steelhead juvenile rearing) Steelhead juvenile rearing Fall chum spawning in current known distribution, otherwise coho spawning Steelhead spawning September November December January February July August September November December January February July August August September October January February July 22

Middle Fork Nooksack USGS Gage #12208000 January Flow Duration Curve Periods of Record: 1920-1921, 1934-1935, 1954, 1964-1968, 1969-1970, 1992-2003. Years of Record: 19 5000 4500 4000 3500 3000 Flow (CFS) 2500 2000 1500 1,200 cfs 1000 500 175 cfs 0 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Percent Exceedence 23

Decision Support Information 24

Comparison of Recommended Instream Flow and Flow Exceeded 10%, 50%, and 90% of the Time With USU Flows for Variable Maximum Percentage of Available Habitat: Middle Fork Nooksack River Site 1200 1000 800 Discharge (cfs) 600 400 200 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Month IFRecom 100% Max Habitat 99% Max Habitat 95% Max Habitat 90% Max Habitat 85% Max Habitat 10% Exceedence Flow 50% Exceedence Flow 90% Exceedence Flow 25

Comparison of Recommended Instream Flow and Flow Exceeded 10%, 50%, and 90% of the Time With USU Flows for Variable Maximum Percentage of Available Habitat: Bertrand Creek 180 160 140 120 Discharge (cfs) 100 80 60 40 20 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Month IFRecom 100% Max Habitat 99% Max Habitat 95% Max Habitat 90% Max Habitat 85% Max Habitat 10% Exceedence Flow 50% Exceedence Flow 90% Exceedence Flow 26

Stratification/Extrapolation 27

28

29

URice: Cluster 1 Oct Jan Apr Jul Month UR: Cluster 2 Oct Jan Apr Jul Month BRl: Cluster 3 Oct Jan Apr Jul Month BRm: Cluster 4 Oct Jan Apr Jul Month 30-1.0 0.0 1.0 Zscores of MMFs -1.0 0.0 1.0 Zscores of MMFs Zscores of MMFs -1.0 0.0 1.0 2.0 Zscores of MMFs -1.0 0.0 1.0 2.0 BRh: Cluster 5 Oct Jan Apr Jul Month BL: Cluster 6 Oct Jan Apr Jul Month ULw: Cluster 7 Oct Jan Apr Jul Month ULn: Cluster 8 Oct Jan Apr Jul Month Zscores of MMFs -1.0 0.0 1.0-1.5-0.5 0.5 Zscores of MMFs Zscores of MMFs -1.0 0.0 1.0 Zscores of MMFs -0.5 0.5 1.5

31

Selection and Adoption Action Plan 32

Concentric Circle Model of Consensus Decision-Making Intergovernmental Working Group (City of Bellingham, Whatcom County, PUD No.1, Lummi Nation, Nooksack Indian Tribe, Ecology, Washington Department of Fish & Wildlife, NOAA, USFS, and EPA) Planning Unit (Governmental and water interest caucus representatives) WRIA wide Affected Parties 33

Government to Government Negotiated Settlement (Federal, State, Tribes) Ecology Instream Flow Rulemaking Technical Work Intergovernmental Instream Flow Working Group Develops initial flow recommendations to be approved by the Joint Board and Planning Unit WRIA 1 Planning Unit - Involved in initial target flow development. - Take actions to improve conditions, e.g., conservation, reuse Interested and affected Parties in Drainages - Involved in initial target flow development. - Take actions to improve conditions, e.g., conservation, reuse = WRIA 1 Project RCW 90.82 Process = Settlement Negotiation Process = State Rule Making Process 34

Start Establish Intergovernmental Instream Flow Working Group Complete Technical Work to Identify Ecological Flow Regime, Current and Future Outof-Stream Needs; Begin Identifying Initial Target Flows for the Drainage Provide Pertinent Information to Affected Parties and Provide Opportunities for Affected Parties to Ask Questions, Identify Their Needs, and Discuss Management Options No Is there Enough Water? No Identify Actions to Reduce Out-of-Stream Needs or Increase Supply and/or Storage Is there Enough Water? No Evaluate the Effects of Reduced Initial Target Flows on Fish Habitat Is there Enough Water? Yes Yes Yes End Flow Regime Acceptable to Parties Identified Proceed to Adoption Process End Flow Regime Acceptable to Parties Identified Proceed to Adoption Process End Flow Regime Acceptable to Parties Identified Proceed to Adoption Process 35

36

Schedule/Next Steps Extrapolation Methods Reports due in February 2006 All preliminary draft reports from USU due on March 17, 2006; comments on preliminary draft reports due on April 21, 2006 All draft reports from USU due on June 9, 2006; comments on draft reports due July 14, 2006. All Final Draft 1 reports submitted to Independent Peer Review panel on August 25, 2006; Peer Review panel comments due by November 3, 2006. All Final Draft 2 reports from USU due on January 5, 2007; Final Approval February 9, 2007 37

Schedule/Next Steps Pilot Flow Negotiations for Middle Fork Nooksack and Bertrand Creek continue during 2006 February 9, 2006, City of Bellingham to identify out-of-stream needs. Out-of-stream needs to be identified for Bertrand Creek during Spring 2006; start pump and dump test Spring 2006. 38

Summary 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 habitats upon which fish rely. An essential step in achieving this goal is to develop the technical information necessary to evaluate instream and out-of-stream needs. 39

Summary This technical information must be evaluated in light of legal and policy considerations to determine how to meet the overall goal of the WRIA 1 Watershed Management Project. The goal of the instream flow analysis element of the WRIA 1 Watershed Management Project is to accurately estimate the relationship between stream flow and fish habitat quantity and quality for different fish species and life stages, and the maintenance of ecological health at selected locations throughout WRIA 1. 40