Implementation of California Coastal Salmonid Monitoring in the Russian River Watershed (2015- 2019) Final Report to the California Department of Fish and Wildlife, Fisheries Restoration Grants Program, Grantee Agreement: P1430411 Sonoma County Water Agency (Sonoma Water) 404 Aviation Boulevard Santa Rosa, California 95403 California Sea Grant 600 American Way, Suite 1 Windsor, CA 95492 February 28, 2019 Suggested citation: Sonoma Water and California Sea Grant. 2019. Implementation of California Coastal Salmonid Population Monitoring in the Russian River Watershed. Santa Rosa, CA. 72 pp. + appendices. Contributors: Sonoma Water: Gregg Horton, Aaron Johnson, Andrea Pecharich, Justin Smith California Sea Grant: Mariska Obedzinski, Andy McClary, Andrew Bartshire, Nick Bauer Table of contents Table of contents .........................................................................................................................i List of tables ................................................................................................................................ ii List of figures ............................................................................................................................. iii List of appendices ....................................................................................................................... v Executive summary .................................................................................................................... 1 Introduction ................................................................................................................................ 4 Project area ............................................................................................................................ 4 Salmonid populations ............................................................................................................. 5 Project goals........................................................................................................................... 5 Data collection, QA/QC and storage ....................................................................................... 6 Chapter I. Sample frame and rotating panels ........................................................................ 8 Introduction ............................................................................................................................ 8 Methods and Results .............................................................................................................. 8 Species and life stage assignments ...................................................................................11 Basinwide Coho Salmon and steelhead adult sampling .....................................................15 Juvenile Coho Salmon sampling ........................................................................................15 Rotating panels ..................................................................................................................16 Discussion .............................................................................................................................20 Chapter II. Life cycle monitoring ............................................................................................21 Introduction ...........................................................................................................................21 Methods ................................................................................................................................21 Adult abundance ................................................................................................................21 Redd abundance ................................................................................................................22 Smolt abundance ...............................................................................................................25 Results ..................................................................................................................................35 Adult abundance ................................................................................................................35 Redd abundance ................................................................................................................38 Smolt abundance ...............................................................................................................42 Discussion .............................................................................................................................49 Adult abundance ................................................................................................................49 Redd abundance ................................................................................................................50 Smolt abundance ...............................................................................................................50 Attachment 3, Grant Agreement No. P1430411 i Chapter III. Basinwide monitoring ...........................................................................................55 Introduction ...........................................................................................................................55 Methods ................................................................................................................................55 Redd abundance (basinwide) .............................................................................................55 Juvenile Coho Salmon spatial structure .............................................................................55 Results ..................................................................................................................................56 Redd abundance (basinwide) .............................................................................................56 Juvenile Coho Salmon spatial structure .............................................................................63 Discussion .............................................................................................................................65 Conclusions and recommendations ..........................................................................................67 Acknowledgements ...................................................................................................................69 References ...............................................................................................................................70 Appendices ...............................................................................................................................73 List of tables Table I-1. Number of reaches by species-life stage stratum in the Russian River watershed as of February, 2019. .........................................................................................................................16 Table I-2. Coho adult rotating panel design. Shaded panels represent panels sampled for a given year. See Appendix A for tributaries and reaches in each panel. .....................................17 Table I-3. Steelhead rotating panel design. Shaded panels represent panels sampled for a given year. See Appendix A for tributaries and reaches in each panel. ..............................................18 Table I-4. Example of dynamic assignment of reaches to panels in adult steelhead stratum. Reaches unable to survey and reaches to fill the panel beyond the 2018/19 season are yet to be determined (TBD). ....................................................................................................................20 Table II-1. Number of salmonid sp (fish >46 cm) and species assignments of Dry Creek DIDSON counts based on proration and historical run-timing from video observations at Sonoma Water’s Mirabel dam in Forestville (Chinook adult LCS, rkm 39.67). ...........................36 Table II-2. Summary of the life cycle monitoring spawner survey effort in Dry Creek tributaries. .................................................................................................................................................38 Table II-3. Calibration ratios (Ry) used to generate estimates for the population of juvenile steelhead in tributaries to Dry Creek during the late summer/early fall in 2017 and 2018. .........46 Table II-4. Year and stream of PIT-tagging and number of fish detected at the mouth of Dry Creek and Mill Creek during the ensuing steelhead emigration period of November 1 through June 30. ....................................................................................................................................48 Table II-5. Estimated number of steelhead pre-smolt emigrants from mainstem Dry Creek and Mill Creek. .................................................................................................................................49 Table III-1. Summary of basinwide spawner survey effort. ........................................................57 Attachment 3, Grant Agreement No. P1430411 ii Table III-2. Coho YOY occupancy estimates and proportion of area occupied from 2015 through 2018. .........................................................................................................................................63 List of figures Figure I-1. Russian River watershed and CMP sample frame. ..................................................10