Russian River Biological Opinion Status and Data Report Year 2016 - 2017 June 2020 Suggested Citation J.Martini-Lamb and Manning, D.J., editors. 2020. Russian River Biological Opinion status and data report year 2016. Sonoma County Water Agency, Santa Rosa, CA. 315 p. Contributors Chapter 1 Jessica Martini-Lamb Chapter 2 Barry Dugan Chapter 3 Jessica Martini-Lamb Chapter 4 Jessica Martini-Lamb, Chris Delaney, Jeff Church, Keenan Foster, Charles Simenstad, William Matsubu, Gregg Horton, Justin Smith, David Cook, Andrea Pecharich Chapter 5 David Cuneo, David Manning, Neil Lassettre, Gregg Horton, Justin Smith, Andrea Pecharich Chapter 6 David Cuneo Chapter 7 Gregg Horton Chapter 8 David Cuneo, David Manning Chapter 9 David Cook, Justin Smith, Shawn Chase Chapter 10 Gregg Horton, Justin Smith Affiliations Shawn Chase, M.S., Senior Environmental Specialist, SCWA Jeff Church, Senior Environmental Specialist, SCWA David Cook, M.A., Senior Environmental Specialist, SCWA David Cuneo, Principal Environmental Specialist, SCWA Chris Delaney, P.E., Water Agency Engineer IV, SCWA Barry Dugan, Principal Programs Specialist, SCWA Keenan Foster, Principal Environmental Specialist, SCWA Gregg Horton, Ph.D., Principal Environmental Specialist, SCWA Neil Lassettre, Ph.D., Principal Environmental Specialist, SCWA David Manning, M.S., Environmental Resources Manager, SCWA Jessica Martini-Lamb, Environmental Resources Manager, SCWA William Matsubu, Ph.D., University of Washington Andrea Pecharich, M.A., Senior Environmental Specialist, SCWA Charles Simenstad, M.S., Professor, University of Washington Justin Smith, Senior Environmental Specialist, SCWA Accessibility Statement For accessibility assistance with this document, please contact Sonoma County Water Agency, Environmental Resources at (707) 526-5370, Fax to (707) 544-6123 or through California Relay Service by dialing 711. Table of Contents CHAPTER 1: Introduction .......................................................................................................... 1-1 References ........................................................................................................................ 1-2 CHAPTER 2: Public Outreach ……………………………………………….……………..………..2-1 Biological Opinion Requirements ...................................................................................... 2-1 Water Agency Public Outreach Activities – 2016 .............................................................. 2-1 Meetings ......................................................................................................................... 2-1 Other Outreach .............................................................................................................. 2-2 CHAPTER 3: Pursue Changes to Decision 1610 Flows ............................................................ 3-1 Permanent Changes ......................................................................................................... 3-2 Summary Status ............................................................................................................. 3-2 Temporary Changes ......................................................................................................... 3-2 Summary Status ............................................................................................................. 3-4 References ........................................................................................................................ 3-4 CHAPTER 4: Estuary Management ........................................................................................... 4-1 Barrier Beach Management .............................................................................................. 4-2 Adaptive Management Plan .............................................................................................. 4-2 Beach Topographic Surveys ............................................................................................. 4-2 2016 Beach and River Mouth Conditions .......................................................................... 4-3 Lagoon Management Season Closures, Outlet Channel Implementation, and Self- Breaches .................................................................................................................. 4-3 Artificial Breaching .......................................................................................................... 4-11 Jetty Study ...................................................................................................................... 4-18 Flood Risk Management Study ....................................................................................... 4-19 Pinniped Annual Monitoring ............................................................................................ 4-20 Conclusions and Recommendations ............................................................................... 4-22 References ...................................................................................................................... 4-22 4.1 Water Quality Monitoring ................................................................................................... 4-25 Methods .......................................................................................................................... 4-25 Continuous Multi-Parameter Monitoring ....................................................................... 4-25 Grab Sample Collection ............................................................................................... 4-27 Results ............................................................................................................................ 4-29 Salinity .......................................................................................................................... 4-31 i Temperature ................................................................................................................. 4-38 Dissolved Oxygen ........................................................................................................ 4-45 Hydrogen Ion (pH) ........................................................................................................ 4-53 Grab Sampling ............................................................................................................. 4-57 Conclusions and Recommendations ............................................................................... 4-72 Continuous Water Quality Monitoring Conclusions ...................................................... 4-72 Water Quality Grab Sampling Conclusions .................................................................. 4-75 References ...................................................................................................................... 4-78 4.2 Algae Sampling .................................................................................................................. 4-80 Methods .......................................................................................................................... 4-80 Algal Estuary Response and Ambient Monitoring ........................................................ 4-80 Results ............................................................................................................................ 4-84 Estuary Closure Algal Response ................................................................................. 4-84 Discussion/Observations ................................................................................................. 4-87 Green Algae ................................................................................................................. 4-89 Golden Brown Algae .................................................................................................... 4-90 Cyanobacteria .............................................................................................................. 4-90 Blooms ......................................................................................................................... 4-90 Estuary Closure Algal Response ................................................................................. 4-91 Recommendations .......................................................................................................... 4-92 References ...................................................................................................................... 4-94 4.3 Invertebrate Prey Monitoring, Salmonid Diet Analysis and Juvenile Steelhead Behavior…...…………………………………………………………………………………….4-95 Methods .......................................................................................................................... 4-96 Sampling Sites ............................................................................................................. 4-97 Juvenile Salmon Diet Composition .............................................................................. 4-98 Prey Resource Availability ........................................................................................... 4-98 Sample Processing and Analyses .............................................................................. 4-103 Results .......................................................................................................................... 4-105 Estuary Conditions ..................................................................................................... 4-105 Juvenile Steelhead Diet Composition .......................................................................