Chinook Salmon (Oncorhynchus tshawytscha) Adult Abundance Monitoring in the Secesh River and Lake Creek, Idaho Annual Report 2005 June 2006 DOE/BP-00020615-1 This Document should be cited as follows: Kucera, Paul, Rick Orme, "Chinook Salmon (Oncorhynchus tshawytscha) Adult Abundance Monitoring in the Secesh River and Lake Creek, Idaho", 2005 Annual Report, Project No. 199703000, 106 electronic pages, (BPA Report DOE/BP-00020615-1) Bonneville Power Administration P.O. Box 3621 Portland, OR 97208 This report was funded by the Bonneville Power Administration (BPA), U.S. Department of Energy, as part of BPA's program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. The views in this report are the author's and do not necessarily represent the views of BPA. Chinook Salmon (Oncorhynchus tshawytscha) Adult Abundance Monitoring in Lake Creek and Secesh River, Idaho in 2005 Annual Report January 2005 – December 2005 Prepared by: Paul A. Kucera and Rick W. Orme Nez Perce Tribe Department of Fisheries Resources Management Lapwai, ID 83540 Prepared for: U.S. Department of Energy Bonneville Power Administration Environment, Fish and Wildlife P.O. Box 3621 Portland, OR 97208-3621 Project Number 199703000 Contract Number 00020615 June 2006 TABLE OF CONTENTS TABLE OF CONTENTS................................................................................................................. i CHAPTER 1 Chinook Salmon (Oncorhynchus tshawytscha) Adult Abundance Monitoring in Lake Creek....................................................................................................1 ABSTRACT.....................................................................................................................................2 TABLE OF CONTENTS.................................................................................................................4 LIST OF FIGURES .........................................................................................................................5 LIST OF TABLES...........................................................................................................................7 ACKNOWLEDGMENTS ...............................................................................................................9 INTRODUCTION .........................................................................................................................10 DESCRIPTION OF PROJECT AREA..........................................................................................12 METHODS ....................................................................................................................................14 TIMING AND ABUNDANCE..................................................................................................14 Equipment .............................................................................................................................. 14 Procedure................................................................................................................................ 15 RESULTS AND DISCUSSION....................................................................................................20 ABUNDANCE ...........................................................................................................................20 POTENTIAL SOURCE OF ERRORS IN UNDERWATER VIDEO MONITORING ..........................................................................................................................24 MIGRATION TIMING..............................................................................................................25 Chinook Salmon..................................................................................................................... 25 Bull Trout............................................................................................................................... 28 REDD COUNTS ........................................................................................................................29 FISH PER REDD .......................................................................................................................32 ACCURACY OF REDD COUNT EXPANSIONS ...................................................................35 STREAM TEMPERATURE AND DISCHARGE ....................................................................39 RECOMMENDATIONS...............................................................................................................40 LITERATURE CITED ..................................................................................................................41 APPENDIX A................................................................................................................................46 CHAPTER 2 Use of Dual Frequency Identification Sonar to Determine Adult Chinook Salmon (Oncorhynchus tshawytscha) Abundance in the Secesh River.............................58 ABSTRACT...................................................................................................................................59 TABLE OF CONTENTS...............................................................................................................60 LIST OF TABLES.........................................................................................................................61 LIST OF FIGURES .......................................................................................................................62 ACKNOWLEDGMENTS .............................................................................................................63 INTRODUCTION .........................................................................................................................64 DESCRIPTION OF STUDY AREA .............................................................................................65 METHODS ....................................................................................................................................65 Dual Frequency Identification Sonar (DIDSON) Operation......................................................68 DIDSON Motion Detection........................................................................................................70 Abundance Estimation................................................................................................................71 Validation ...................................................................................................................................76 Listed Chinook Salmon Population Assessment........................................................................77 RESULTS AND DISCUSSION....................................................................................................77 i Abundance Estimation................................................................................................................77 Potential Sources of Error in DIDSON Abundance Monitoring................................................79 Migration Timing .......................................................................................................................81 Validation Monitoring................................................................................................................82 DIDSON Operations ..................................................................................................................83 LISTED CHINOOK SALMON POPULATION STATUS ..........................................................85 RECOMMENDATIONS...............................................................................................................87 LITERATURE CITED ..................................................................................................................89 APPENDIX B ................................................................................................................................93 ii CHAPTER 1 Chinook Salmon (Oncorhynchus tshawytscha) Adult Abundance Monitoring in Lake Creek Annual Report January 2005 – December 2005 Prepared by: Paul A. Kucera and Rick W. Orme Nez Perce Tribe Department of Fisheries Resources Management Lapwai, ID 83540 Prepared for: U.S. Department of Energy Bonneville Power Administration Environment, Fish and Wildlife P.O. Box 3621 Portland, OR 97208-3621 Project Number 199703000 Contract Number 00020615 June 2006 ABSTRACT Underwater time lapse video technology was used to determine tributary specific adult spring and summer chinook salmon abundance in Lake Creek in 2005. In 2005, the first upstream salmon passage occurred on June 25, 14 days after installation of the fish counting station. Total wild and hatchery salmon abundance in Lake Creek was 140 fish, with 95% confidence intervals of ± 2 fish. Wild salmon abundance was estimated to be 138 adults. Estimated hatchery fish composition represented 1.5% of the spawning population. Chinook salmon jacks comprised an estimated 5.3% of the run. There was an estimated 1.77 fish per redd in Lake Creek in 2005. The salmon spawning migration in Lake Creek occurred from June 25 to September 4 with a total of 576 fish passages observed at the fish counting station. Median net upstream salmon passage was observed on July 13, and the maximum number of net upstream migrating salmon were in the Lake Creek system by August 23. Adult salmon moved freely upstream and downstream through the fish