Eel River Recovery Project Final Report: Citizen Assisted 2015-2016 Fall Chinook Salmon Monitoring Prepared for: Eel River Recovery Project By: Patrick Higgins, ERRP Managing Director & Eric Stockwell, ERRP Fall Chinook Project Coordinator With Funding From: Patagonia World Trout Initiative & Salmon Restoration Association Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 i Acknowledgements The Eel River Recovery Project (ERRP) faced challenging conditions in estimating the 2015- 2016 Eel River fall Chinook salmon run due to extremely low flows in early fall and then very high flows starting in December. ERRP wishes to thank the Wiyot Tribe and Humboldt Redwood Company for once again co-sponsoring the project. The project was made possible by grant funding provided by the Patagonia World Trout Initiative and the Salmon Restoration Association, which sponsors the World’s Largest Salmon BBQ in Fort Bragg. ERRP was assisted by dozens of volunteers who participated in lower Eel River dive surveys and in tracking fall Chinook migrations and spawning throughout the watershed. Only three dives were carried out from late October to mid-November in the lower river and only in the 12th Street Pool because of shallow depths, profuse algae and the risk of divers contracting swimmer’s itch. When November rains remained sparse, ERRP deployed kayaks for lower main Eel River spawning surveys. Results from the Van Arsdale Fish Station and aerial and ground surveys of spawning were shared by fisheries biologist Scott Harris of the California Department of Fish and Wildlife (CDFW). Thanks go out to Park Steiner and PG&E (SEC 2016) for sharing spawning data from the upper Eel River and Tomki Creek, although the latter had no fish sightings this year. The big story on this year’s run was that Chinook salmon became diseased while holding in lower Eel River pools which lead to blindness. ERRP wishes to thank the local press and electronic media for covering this problem including KMUD radio, KAEF TV, KIEM TV, Redwood Times, the Independent, and the Eureka Times Standard. Reporters Will Houston of the Times Standard and Keith Easthouse of the Independent deserve special mention for their in- depth coverage of the salmon project. ERRP worked cooperatively with CDFW to capture diseased fish for analysis, and we wish to thank Alan Renger of the Fortuna Office for his initiative. Professor Esteban Soto of the University of California, Davis rendered important assistance in analyzing the cause of disease and ERRP is also very appreciative of UCD efforts. Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 ii ERRP Thanks 2015-2016 Volunteers & the Community for Support David Sopjes Dave Wagner Sal Steinberg Ernie Merrifield Paul Trichilo Bruce Hilbach-Barger Diane Higgins Dane Downing Paul Domanchuk Dennis Halligan Walker Wise Cathy Warren Greg Byers Larry Bruckenstein Graham and Dotti Russell Doug Parkinson Karen & Scott Walsh Jeff Wells Sharon & Dean Edell Dorje Bond Seth Rick Brandi Easter Sunshine Johnston Jason Webster John Evans/Big Bend Lodge Sam Parker Jeff Hedin Brandon Torske Jim Williams Nolan Cahill Stephen Kullman Bernabe Alvirez Tim Nelson Eric Johnston Domenic Belli Mickey Bailey Jason Webster Talia Rose Willie Grover David Bradfield Sage Halvorson Bernabe Alvidrez Sean Croft Nolan Cahill Tyler Grunert Kevin Silver Jesse Barrer Ashley Woodford Barbara Sopjes Kenny Priest Amy Conway Stephanie Sawyer Richard Geinger Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 iii Table of Contents Cover……………………………………………………………………………………. i Acknowledgements……………………………………………………………………... ii Table of Contents……………………………………………………………………...... iii Executive Summary………………………………………………………………………..1 Background ………………………………………………………………………………..2 Time, Location and Conditions of Surveys………………………………………………2-4 Methods ………………………………………………………………………………….2-5 Lower Eel River Pool Data ……………………………………………………..…2 Dive Surveys……………………………………………………………………….5 Kayak Surveys......…………………....…………………………………................5 Tributary Surveys…………………....…………………………………..................5 Volunteer Observations…………………………………………………………….5 Van Arsdale Fish Station ……………………………………………………..……5 Results …………………………………………………………………………………5-12 Pool Depths, Temperature, and Dissolved Oxygen ……………………………...5-7 Kayak Surveys of Lower Eel River Pools …………………………………………7 Spawner Surveys from Kayaks………………………………………………….8-10 Tributary Surveys…………………………………………………………………...9 Van Arsdale Fish Station Chinook Salmon Counts……………………………..9-11 Volunteer Observations ..………………………………………………………11-12 Discussion .…………………………………………………………………..................13-20 Precision of ERRP Run Estimate …………………………………………………13 Lower Eel River Bed Scour and Chinook Egg and Alevin Survival………………13 Tributary Habitat Impairment……………………………………………………...14 Chinook Salmon Disease Outbreak …………………………………………….14-16 Lower Eel and Van Duzen River Habitat Conditions ………………………...16-17 Lower Eel and Van Duzen River Restoration Opportunities……………………16-18 Poaching and Driving Through Redds ………………………………………… 17-19 Chinook Salmon Run Trends 2012-2015.……………………………………… 19-20 Prospects for Rebound in 2016-2017…………………………………………….....19 Conclusion ………………………………………………………………………………….20 Recommendations …………………………………………………………………………..21 References ………………………………………………………………………………22-23 Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 iv Executive Summary ERRP has successfully estimated the Eel River fall Chinook run since 2012, and each year is unique and has different challenges. The 2015-2016 citizen assisted monitoring project was the most difficult, however, because early rains failed and dives were not able to be scheduled, and then rainfall was so high after December 1 that observation of migrating and spawning Chinook salmon were limited for protracted periods. Despite the El Nino conditions in the ocean that are usually linked to increased precipitation, rains from September through November were extremely sparse. Lower Eel River flows as measured by the U.S. Geologic Survey at Scotia did not exceed 100 cfs until November 11, which limited fish passage and prevented normal fall flushing of algae beds. Algae impairs visibility and harbors swimmers itch organisms. Consequently, dive surveys were restricted to the 12th Street Pool that is deeper and mixed by winds and other pools were surveyed by kayak. Early run Eel River fall Chinook were restricted to the estuary during late August and early September as flows at Scotia were only just over 30 cfs. ERRP documented movement of fish upstream as far as the 12th Street Pool by September 21 after light rains, but the major influx into lower river pools was with extremely high tides from October 22-24. Hundreds of Chinook salmon sat in shallow, algae infested pools and about 10% of early run fish went blind as a result of a fluke attacking their eyes. Dives on October 31, November 7 and November 14 estimated that 920, 1000, and 1200 Chinook salmon were holding, respectively, with approximately 25% of the fish comprised of smaller jack salmon. ERRP estimated 5,000 Chinook salmon were holding in the lower Eel River from the 12th Street Pool downstream on November 14. Extensive Chinook salmon spawning in the main Eel River downstream of Dyerville was documented by ERRP from November 11 through December 1. Before December 1, Chinook salmon access to headwaters was limited with spawning on the main Eel below Dos Rios, the South Fork below Leggett, and the Van Duzen River downstream of Goat Rock Falls. After December 1, flows were adequate for access and spawners were seen in low numbers throughout the basin, including upper Outlet Creek, Ten Mile Creek, the Middle Fork and Black Butte River, and the upper South Fork near Branscomb. Lower South Fork Eel River tributaries showed a late fall Chinook run peak in mid-December. Chinook arrived at the Van Arsdale Fish Station on December 6, and only 102 fish passed upstream to spawn during the entire season. Spawners were noted in Ten Mile Creek and upper Outlet Creek, but none were seen in Tomki Creek (SEC 2016). ERRP once again found that sediment impairment limited spawning use of a number of other Eel River tributaries. ERRP used historic run timing and professional judgment regarding fish response to flows to arrive at an estimate for the 2015-2016 late run of 5,000-10,000 fish. The total 2015-2016 Eel River fall Chinook run total estimate is 10,000-15,000. The population is showing a declining trend since 2012, but remains above 10,000 fish and at no risk of loss of genetic diversity. High jack counts indicate another strong year class and improved ocean conditions and restricted ocean fisheries may also favor population rebuilding in 2016-2017. However, ERRP has concern about survival of adult Chinook salmon in the lower Eel River due to poor holding habitat, and strongly encourages expeditious restoration to improve conditions. Eel River Recovery Project: Final Report 2015-2016 Fall Chinook Salmon Monitoring July 2016 1 Background ERRP community scoping meetings in September 2011 highlighted concerns about the potential loss of native Eel River fall Chinook salmon. People expressed frustration over the lack of data available from agencies and wanted more information on fish population trends. Since agency budgets are limited and they lack capacity to collect more data on Chinook salmon population trends, ERRP began volunteer