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Determination and Evaluation of Habitat – Flow Relationships in the Sultan River, Washington - Sultan River Instream Flow Study – RSP 3 - Prepared for: Public Utility District No. 1 of Snohomish County and City of Everett Prepared by: R2 Resource Consultants, Inc. 15250 N.E. 95th Street Redmond, Washington 98052 March 19, 2009 Determination and Evaluation of Habitat – Flow Relationships in the Sultan River, Washington - Sultan River Instream Flow Study – RSP 3 - Prepared for: Public Utility District No. 1 of Snohomish County and City of Everett Prepared by: Dudley W. Reiser, Michael R. Gagner, Chi-Ming Huang, Catherine Morello Timothy J. Sullivan, Stuart M. Beck, and Timothy L. Nightengale R2 Resource Consultants, Inc. 15250 N.E. 95th Street Redmond, Washington 98052 March 19, 2009 Sultan River Instream Flow Study – RSP 3 CONTENTS EXECUTIVE SUMMARY ....................................................................................................... XVI 1. INTRODUCTION ................................................................................................................. 1-1 1.1 STUDY OBJECTIVES.......................................................................................................... 1-3 1.2 LINKAGES TO OTHER STUDIES ......................................................................................... 1-4 1.3 REPORT ORGANIZATION AND CONTENT ........................................................................... 1-6 2. BACKGROUND INFORMATION ...................................................................................... 2-1 2.1 DESCRIPTION OF STUDY AREA AND STUDY REACHES...................................................... 2-1 2.1.1 Study Area........................................................................................................... 2-2 2.1.2 Sultan River Study Reaches ................................................................................ 2-2 2.1.2.1 Operational Reach 3................................................................................ 2-3 2.1.2.2 Operational Reach 2................................................................................ 2-4 2.1.2.3 Operational Reach 1................................................................................ 2-5 2.2 PROJECT FACILITIES AND CURRENT OPERATIONS ............................................................ 2-6 2.2.1 Project Facilities .................................................................................................. 2-6 2.2.1.1 Culmback Dam ....................................................................................... 2-6 2.2.1.2 Diversion Dam........................................................................................ 2-7 2.2.1.3 Powerhouse............................................................................................. 2-9 2.2.2 Project Operations ............................................................................................... 2-9 2.2.3 Instream Flow Studies and Flow Releases ........................................................ 2-13 2.2.4 Downramping Rates .......................................................................................... 2-15 2.3 FISH OF THE SULTAN RIVER ........................................................................................... 2-17 2.3.1 CHINOOK SALMON (Oncorhynchus tshawytscha) ....................................... 2-17 2.3.2 COHO SALMON (Oncorhynchus kisutch)....................................................... 2-20 2.3.3 PINK SALMON (Oncorhynchus gorbuscha)................................................... 2-21 2.3.4 CHUM SALMON (Oncorhynchus keta)........................................................... 2-22 2.3.5 STEELHEAD TROUT (Oncorhynchus mykiss)............................................... 2-23 2.3.6 BULL TROUT (Salvelinus confluentus)........................................................... 2-24 2.3.7 COASTAL CUTTHROAT TROUT (Oncorhynchus clarki clarki) ................. 2-26 3. METHODS ............................................................................................................................ 3-1 R2 Resource Consultants, Inc. iii March 19, 2009 1628.07/Instream Flow Report_031909 Sultan River Instream Flow Study – RSP 3 3.1 PLANNING AND SITE RECONNAISSANCE........................................................................... 3-1 3.2 STUDY REACH DELINEATION AND TRANSECT SELECTION ............................................... 3-3 3.2.1 Mainstem Transect Selection .............................................................................. 3-4 3.2.2 Side Channel Transect Selection......................................................................... 3-5 3.3 FIELD DATA COLLECTION .............................................................................................. 3-14 3.3.1 Hydraulic and Habitat Measurements ............................................................... 3-14 3.4 HABITAT SUITABILITY CRITERIA.................................................................................... 3-27 3.4.1 Snorkel Surveys................................................................................................. 3-27 3.4.2 Redd Surveys..................................................................................................... 3-27 3.4.3 Data Analysis..................................................................................................... 3-28 3.4.4 Review and Adoption of HSC Criteria.............................................................. 3-28 3.5 MODELING ..................................................................................................................... 3-30 3.5.1 Hydraulic Modeling........................................................................................... 3-30 3.5.2 Habitat Modeling............................................................................................... 3-31 3.5.2.1 Transect Weighting and Habitat Mapping............................................. 3-31 3.5.3 Flow and Habitat Time Series ........................................................................... 3-34 3.5.3.1 Flows in Operational Reach 3............................................................... 3-35 3.5.3.2 Flows in Operational Reach 2............................................................... 3-35 3.5.3.3 Flows in Operational Reach 1............................................................... 3-35 4. HABITAT MODELING........................................................................................................ 4-1 4.1 REACH 3 – CULMBACK DAM TO DIVERSION DAM............................................................ 4-2 4.1.1 PHABSIM Analysis ............................................................................................ 4-2 4.1.1.1 Spawning Habitat.................................................................................... 4-2 4.1.1.2 Juvenile and Adult Habitat...................................................................... 4-2 4.1.1.3 Habitat Time Series................................................................................. 4-9 4.2. REACH 2 – DIVERSION DAM TO POWERHOUSE ................................................................ 4-9 4.2.1 PHABSIM Analysis .......................................................................................... 4-20 4.2.1.1 Spawning............................................................................................... 4-20 4.2.1.2 Juvenile and Adult Habitat.................................................................... 4-20 4.2.1.3 Habitat Time Series............................................................................... 4-27 4.3 REACH 1 – POWERHOUSE TO SKYKOMISH RIVER ........................................................... 4-27 R2 Resource Consultants, Inc. iv March 19, 2009 1628.07/Instream Flow Report_031909 Sultan River Instream Flow Study – RSP 3 4.3.1 Mainstem PHABSIM Analysis .......................................................................... 4-27 4.3.1.1 Spawning Habitat................................................................................... 4-27 4.3.1.2 Juvenile and Adult Habitat.................................................................... 4-34 4.3.1.3 Habitat Time Series............................................................................... 4-34 4.3.2 Side Channel Habitat:Flow Analysis................................................................. 4-41 5. SUMMARY........................................................................................................................... 5-1 6. REFERENCES ...................................................................................................................... 6-1 Appendix I – Data QA/QC Notes APPENDIX A: Transect Selection Presentation – June 12, 2008 APPENDIX B: Target Flow Memorandum – June 11, 2007 APPENDIX C: Habitat Suitability Criteria (HSC) – includes a) Proposed Habitat Suitability Criteria (HSC) Curves for Application in Habitat-Flow Modeling for the Sultan River Instream Flow Study – RSP 3, June 5, 2008; b) Technical Memorandum: Sultan River Instream Flow Study – HSC Preference Analysis and Revised Steelhead and Chinook Curves, July 31, 2008; c) HSC curves used in habitat- flow modeling APPENDIX D: Habitat:Flow Relationships and Time Series Analysis APPENDIX E: Transect Photographs APPENDIX F: Transect Cross Sectional Profiles and Model Calibration Details APPENDIX G: Field Notes R2 Resource Consultants, Inc. v March 19, 2009 1628.07/Instream