MAINSTEM CLEARWATER RIVER STUDY: ASSESSMENT FOR SALMONID SPAWNING, INCUBATING, AND REARING Final Report Prepared by Billy D. Arnsberg, Project Leader William P. Connor, Research Biologist Nez Perce Tribe and Edward Connor, Project Manager EBASCO Environmental Other Contributors Markley J. Pishl, Fisheries Technician Marc A. Whitman, Fisheries Technician Prepared For Jeff Gislason, Project Manager U.S. Department of Energy Bonneville Power Administration Division of Fish and Wildlife P.O. Box 3621 Portland, OR 97208-3621 Project No. 88-15 Contract No. DE-BI79-87BP37474 April 1992 The Nez Perce Tribe sub-contracted with EBASCO Environmental during this study to develop capabilities for predicting fish habitat conditions in the lower mainstem Clearwater River under a limited range of discharge regimes from Dworshak Dam. The Nez Perce Tribe used this information to analyze a range of discharges from Dworshak Dam for anadromous fish habitat requirements. The Tribe's analysis does not necessarily reflect views of EBASCO Environmental. Flow analyses provided to the Bonneville Power Administration and/or U.S. Army Corps of Engineers within this report on the lower mainstem Clearwater River shall in no way limit or influence future water rights claims or flow recommendations made by the Nez Perce Tribe for any purposes. Flows analyzed in this report are independent of conditions for upstream or downstream anadromous fish migration and of any other purposes not specifically stated. a TABLE OF CONTENTS Pase ACKNOWLEDGEMENTS........................................ vii EXECUTIVE SUMMARY.......................................viii INTRODUCTION............................................ 1 CHAPTER 1. DESCRIPTION OF PROJECT AREA ................. 3 CHAPTER 2. CHINOOK SALMON AERIAL REDD SURVEYS .......... 13 CHAPTER 3. CHINOOK SALMON EGG INCUBATION TIMING ........ 18 CHAPTER 4. SPAWNING SUBSTRATE QUALITY .................. 26 CHAPTER 5. CHINOOK SALMON SURVIVAL TO HATCH ............ 40 CHAPTER 6. FISH DENSITY ESTIMATES ...................... 49 CHAPTER 7. SMOLT OUTMIGRATION TIMING AND SURVIVAL ...... 61 CHAPTER 8. HYDRAULIC MODEL ............................. 69 CHAPTER 9. FISH SUITABILITY CURVES ..................... 76 CHAPTER 10. HABITAT SIMULATION MODELING ................. 91 CHAPTER 11. SPAWNING HABITAT QUANTIFICATION ............. 118 CHAPTER 12. TEMPERATURE ANALYSIS ........................ 123 CHAPTER 13. CONCLUSIONS AND RECOMMENDATIONS ............. 142 LITERATURE CITED ........................................ 147 APPENDIX A. FISH DENSITY ESTIMATES ...................... 156 APPENDIX B. HYDRAULIC MODEL CALIBRATION ................. 163 APPENDIX C. SUITABILITY CURVE DEVELOPMENT ............... 176 APPENDIX D. HABITAT MODELING PROCEDURE .................. 180 APPENDIX E. RIVER TEMPERATURE MODELING PROCEDURE ........ 187 APPENDIX F. SPAWNING SUBSTRATE MOVEMENT ANALYSIS ........ 194 i LIST OF TABLES Tab 2.1. Fall chinook salmon aerial redd surveys on the lower mainstem Clearwater River............... 15 Tab 2.2. Fall chinook lengths, sex, and percent spawn data.......................................... 15 Tab 3.1. Observed fall and summer chinook incubation timing on the lower mainstem Clearwater River. 21 Tab 4.1. Substrate particle size distribution of freeze-core samples........................... 31 Tab 4.2. Chinook salmon spawning habitat quality indices based on freeze-core samples.......... 34 Tab 4.3. Statistical comparison of mean log transformed fredle index numbers from freeze-core samples. 36 Tab 5.1. Comparison of percent fines and fredle index numbers in intrusion baskets and freeze-cores. 45 Tab 5.2. Artificial redd substrate and water column temperatures.................................. 46 Tab 6.1. Mean fish densities at the North Fork and Big Canyon study sites............................ 55 Tab 6.2. Mean fish densities at the Potlatch River and Bedrock Creek study sites..................... 56 Tab 8.1. Transect groupings employed in IFG4 hydraulic simulations for the LMCR...................... 72 Tab 9.1. Brusven substrate code applied to the lower mainstem Clearwater and other study rivers.... 78 Tab 10.1. Habitat exceedance values for chinook salmon spawning...................................... 112 Tab 10.2. Habitat exceedance values for holding adult chinook salmon................................ 112 Tab 10.3. Habitat exceedance values for chinook salmon juveniles..................................... 112 Tab 10.4. Habitat exceedance values for holding adult steelhead trout............................... 114 Tab 10.5. Habitat exceedance values for rainbow/ steelhead trout juveniles..................... 114 ii LIST OF TABLES (continued) Tab 11.1. Estimated potential chinook salmon redds for the LMCR.................................. 121 LIST OF FIGURES Fig 1.1. Lower mainstem Clearwater River project area.. 4 Fig 1.2. Daily discharge statistics by month for the lower mainstem Clearwater River............... 6 Fig 1.3. Daily discharge statistics by month for Dworshak Reservoir............................ 8 Fig 1.4. Daily discharge statistics by month for the upper mainstem Clearwater River............... 9 Fig 1.5. Daily water temperatures in the upper mainstem, North Fork, and LMCR (June 1 - Dee 31, 1989).. 10 Fig 1.6. Daily water temperatures in the upper mainstem, North Fork, and-LMCR (Jan 1 to Dee-31, 1990).. 11 Fig 2.1. Location and number of fall chinook redds on the lower mainstem Clearwater River........... 16 Fig 3.1. Egg incubation box............................ 20 Fig 3.2. Observed fall and summer chinook salmon incubation timing dates....................... 22 Fig 4.1. Substrate particle size distributions of chinook salmon spawning areas................. 32 Fig 4.2. Comparison of fredle index numbers from freeze-core data.............................. 35 Fig 5.1. Intrusion basket.............................. 42 Fig 6.1. Direct observation lane divided into the SCUBA and snorkeling sublane.................. 52 Fig 6.2. Mean chinook salmon densities in the LMCR by study sites, lggo............................. 57 Fig 6.3. Mean rainbow/steelhead trout densities in the the LMCR by study sites, 1989 and 1990........ 57 Fig 6.4. Mean redside shiner densities in the LMCR by study sites, 1989 and lggo.................... 58 iii LIST OF FIGURES (continued) Fig 6.5. Mean whitefish and sucker densities in the LMCR by study sites, 1989 and 1990............ 58 Fig 7.1. PIT-tagged spring chinook salmon release site. 63 Fig 7.2. Interrogation dates and number of PIT-tagged spring chinook salmon......................... 65 Fig 8.1. Hydraulic subdivision of lower Potlatch island complex................................ 73 Fig 9.1. Composite preference curves for chinook salmon spawning............................... 81 Fig 9.2. Composite suitability curves for adult chinook salmon holding........................ 83 Fig 9.3. Composite preference curves for chinook salmon juveniles.............................. 84 Fig 9.4. Composite preference curves for chinook salmon fry.................................... 86 Fig 9.5. Preference curves for rainbow/steelhead trout juveniles............................... 88 Fig 9.6. Preference curves for rainbow/steelhead trout fry..................................... 90 Fig 10.1. Weighted usable area versus discharge curves for spawning chinook salmon................... 95 Fig 10.2. Weighted usable area versus discharge curves for rainbow/steelhead trout juveniles......... 95 Fig 10.3. Habitat area versus discharge for chinook salmon spawning............................... 96 Fig 10.4. Habitat area versus discharge for adult chinook salmon and steelhead holding.......... 96 Fig 10.5. Habitat area versus discharge for chinook salmon fry.................................... 98 Fig 10.6. Critical temperature habitat area versus discharge for chinook salmon fry.............. 98 Fig 10.7. Habitat area versus discharge for chinook salmon juveniles.............................. 100 iv LIST OF FIGURES (continued) Fig 10.8. Critical temperature habitat versus discharge for chinook salmon juveniles.................. 100 Fig 10.9. Habitat area versus discharge for rainbow/ steelhead trout fry........................... 101 Fig lO.lO.Critical temperature habitat area versus discharge for rainbow/steelhead trout fry..... 101 Fig lO.ll.Habitat area versus discharge for rainbow/ steelhead trout juveniles.................... 103 Fig 10.12.Critical temperature habitat area versus discharge for rainbow/steelhead juveniles.... 103 Fig 10.13.Total habitat area versus discharge curve for chinook salmon spawning....................... 104 Fig 10.14.Total habitat area versus discharge curve for chinook salmon and steelhead trout holding.... 104 Fig 10.15.Total habitat area versus discharge curve for chinook salmon fry............................ 105 Fig 10.16.Critical temperature total habitat area versus discharge curve for chinook salmon fry........ 105 Fig 10.17.Total habitat area versus discharge curve for chinook salmon juveniles...................... 106 Fig 10.18.Critical temperature total habitat area versus discharge curve for chinook salmon juveniles.. 106 Fig 10.19.Total habitat area versus discharge curve for rainbow/steelhead trout fry................... 108 Fig 10.20.Critical temperature total habitat area versus discharge curve for rainbow/steelhead fry..... 108 Fig 10.21.Total habitat area versus discharge curve for rainbow/steelhead trout juveniles............. 109 Fig 10.22.Critical temperature