STUDY PLAN TO ASSESS SHASTA RIVER SALMON AND STEELHEAD RECOVERY NEEDS Prepared by: Shasta Valley Resource Conservation District 215 Executive Court, Suite A Yreka, CA 96097 and McBain & Trush, Inc. 980 7th Street Arcata, CA 95521 Prepared for: U.S. Fish and Wildlife Service Arcata Fish and Wildlife Office 1655 Heindon Road Arcata, CA 95521 September 19, 2013 Study Plan to Assess Shasta River Salmon and Steelhead Recovery Needs September 19, 2013 This page intentionally blank -ii- Study Plan to Assess Shasta River Salmon and Steelhead Recovery Needs September 19, 2013 TABLE OF CONTENTS Page 1. INTRODUCTION ......................................................................................................................................... - 1 - 1.1. STUDY PLAN PURPOSE ............................................................................................................................. - 4 - 1.2. A FRAMEWORK FOR STUDY PLAN DEVELOPMENT ................................................................................... - 4 - 2. FACTORS THAT LIKELY SUSTAINED HISTORICAL SALMONID POPULATIONS ................... - 5 - 2.1. UNIQUE GEOLOGIC AND HYDROLOGIC SETTINGS .................................................................................... - 5 - 2.2. THE UNIMPAIRED ANNUAL HYDROGRAPH .............................................................................................. - 7 - 2.2.1. Zone 1: A Rainfall and Snowmelt Hydrograph ............................................................................ - 12 - 2.2.2. Zone 2: A Spring-Fed Hydrograph .............................................................................................. - 15 - 2.2.3. Zone 3: A Snowmelt and Spring Hydrograph ............................................................................... - 15 - 2.2.4. Zone 4: A Rainfall Hydrograph .................................................................................................... - 15 - 2.2.5. Cumulative Daily Average Hydrographs ..................................................................................... - 16 - 2.2.6. Water Year 2000 Unimpaired Model Simulation for Flow and Water Temperature ................... - 18 - 2.3. DIVERSE SALMONID LIFE HISTORY TACTICS ......................................................................................... - 18 - 2.3.1. Historical Shasta River Life History Tactics ................................................................................ - 19 - 3. CONTEMPORARY STREAMFLOW AND HABITAT CONDITIONS IN THE SHASTA BASIN .. - 22 - 3.1. WATER DEVELOPMENT .......................................................................................................................... - 22 - 3.2. IMPAIRED ANNUAL HYDROGRAPHS ....................................................................................................... - 23 - 3.3. WATER TEMPERATURE CONDITIONS ..................................................................................................... - 27 - 3.3.1. Shasta River Temperature Profile ................................................................................................ - 27 - 3.4. WATER QUALITY STANDARDS ............................................................................................................... - 28 - 3.4.1. Beneficial Uses ............................................................................................................................. - 30 - 3.4.2. Water Quality Objectives ............................................................................................................. - 30 - 3.5. FISH HEALTH IN THE KLAMATH AND SHASTA RIVERS ........................................................................... - 31 - 3.6. CONTEMPORARY SALMONID HABITAT STUDIES .................................................................................... - 31 - 3.6.1. Instream Flow Needs (IFNs) Studies ............................................................................................ - 31 - 3.6.2. Spawning Habitat Evaluations ..................................................................................................... - 32 - 3.6.3. Livestock Exclusion Fencing from Riparian Zone ........................................................................ - 33 - 3.6.4. Priority Actions for Restoration of the Shasta River: Deas et al. (2004) Technical Report ......... - 34 - 3.6.5. Studies on Nelson Ranch and Shasta Big Springs Ranch ............................................................. - 35 - 4. GENERAL STUDY PLAN RECOMMENDATIONS .............................................................................. - 40 - 4.1. RECOMMENDATION #1. FORM A TECHNICAL WORKING GROUP ............................................................ - 40 - 4.2. RECOMMENDATION #2. INSTREAM FLOW NEED RECOMMENDATIONS ................................................... - 40 - 4.3. RECOMMENDATION #3. EVALUATE THE FEASIBILITY OF RECOVERY WITH AND WITHOUT DWINNELL DAM .................................................................................................................................... - 41 - 4.4. RECOMMENDATION #4. SUPPORT ACTIONS FOR IMPROVED KLAMATH RIVER, ESTUARY, AND STOCK HARVEST MANAGEMENT. ..................................................................................................................... - 42 - 5. STUDY PLAN ELEMENTS ....................................................................................................................... - 43 - 5.1. STUDY PLAN ELEMENT #1: WATER BALANCE MODELING .................................................................... - 43 - 5.2. STUDY PLAN ELEMENT #2: PHYSICAL HABITAT ASSESSMENT FOR HIGH PRIORITY LHTS .................... - 44 - 5.3. STUDY PLAN ELEMENT #3: WATER QUALITY ASSESSMENTS ................................................................ - 48 - 5.4. STUDY PLAN ELEMENT #4: RIPARIAN VEGETATION STUDIES ................................................................ - 52 - 5.5. STUDY PLAN ELEMENT #5: JUVENILE AND ADULT MIGRATION ............................................................ - 58 - 5.6. STUDY PLAN ELEMENT #6: GEOMORPHIC ASSESSMENT ........................................................................ - 61 - 5.7. STUDY PLAN ELEMENT #7: SPAWNING GRAVEL ASSESSMENT .............................................................. - 64 - 5.8. STUDY PLAN ELEMENT #8: SALMONID POPULATION STUDIES ............................................................... - 67 - 5.9. STUDY PLAN ELEMENT #9. DEVELOP POPULATION MODEL .................................................................. - 71 - 6. REFERENCES............................................................................................................................................. - 73 - iii Study Plan to Assess Shasta River Salmon and Steelhead Recovery Needs September 19, 2013 7. APPENDICES .............................................................................................................................................. - 84 - 7.1. APPENDIX A: PRIMARY DOCUMENTS REVIEWED DURING PREPARATION OF THIS STUDY PLAN. ............. - 84 - 7.2. APPENDIX B. GENERAL DESCRIPTIONS OF SALMONID LIFE HISTORIES ................................................. - 85 - 7.2.1. Fall-run Chinook Salmon ............................................................................................................. - 85 - 7.2.2. Coho Salmon ................................................................................................................................ - 86 - 7.2.3. Steelhead ...................................................................................................................................... - 88 - 7.2.4. Spring-run Chinook Salmon ......................................................................................................... - 88 - 7.3. APPENDIX C: SALMONID HABITAT REQUIREMENTS ............................................................................... - 90 - 7.3.1. Physical Habitat Requirements for Salmonids ............................................................................. - 90 - 7.3.2. Water Temperature Requirements for Salmonids ......................................................................... - 90 - 7.4. APPENDIX D: SHASTA BASIN HIGH PRIORITY LIFE HISTORY TACTICS IMPORTANT FOR SALMONID RECOVERY ............................................................................................................................................ - 94 - 7.4.1. Tactic 1: Fall-run Chinook Salmon Canyon 0+ Tactic ................................................................ - 96 - 7.4.2. Tactic 2: Fall-run Chinook Salmon Big Springs Complex 0+ Tactic .......................................... - 98 - 7.4.3. Tactic 3: Coho Salmon Big Springs Complex 1+ Tactic ............................................................ - 100 - 7.4.4. Tactic 4: Coho Salmon 0+ Big Springs Complex LHT .............................................................. - 104 - 7.4.5. Tactic 5: Steelhead 1+ and 2+ Big Springs Complex LHT ........................................................ - 106 - 7.4.6. Tactic 6: Steelhead Little Shasta River Headwaters 1+ Tactic .................................................. - 108 - 7.4.7. Tactic 7: Steelhead 2+ Little Shasta River LHT ......................................................................... - 110 - 7.4.8. Tactic 8: Coho Salmon Parks Creek Headwaters Tactic ........................................................... - 114 - 7.4.9. Tactic 9: Coho Salmon Parks