TECHNICAL MEMORANDUM 3-9 Non-ESA Listed Fish Populations Downstream of Englebright Dam Yuba River Development Project FERC Project No. 2246 December 2012 ©2012, Yuba County Water Agency All Rights Reserved Yuba County Water Agency Yuba River Development Project FERC Project No. 2246 TECHNICAL MEMORANDUM 3-9 EXECUTIVE SUMMARY In 2012, Yuba County Water Agency (YCWA) characterized the fish community in the lowermost 24 miles of the Yuba River from the United States Army Corps of Engineer’s Englebright Dam downstream to the confluence of the Yuba River with the Feather River. YCWA identified and reviewed 54 references reporting on existing and ongoing fish studies in the downstream of Englebright Dam and found reliable, documented, and reported occurrences of 42 fish species and anecdotal unverified reports of three species, for a total of 45 fish species.1 Twenty-two species (49% of the total fish species), nine of which are anadromous, are native to California. Twenty-three species (51% of the total fish species), two of which are anadromous, are introduced to California. None of the fish species are catadromous, and none are reported to only occur in the Yuba River basin. Among the fish species documented to occur in the Yuba River downstream of Englebright Dam were three species listed under the federal Endangered Species Act (ESA): 1) Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha) Evolutionary Significant Unit (ESU); 2) Central Valley steelhead (O. mykiss) Distinct Population Segment (DPS); and 3) Southern Distinct Population Segment of North American green sturgeon (Acipenser medirostris). Spring-run Chinook salmon is also listed under the California ESA. Six fish species listed as California Species of Special Concern (CSC) were also documented in the Yuba River downstream of Englebright Dam, including): 1) pink salmon (O. gorbuscha); 2) chum salmon (O. keta) (both native anadromous fish, but extremely rare in Central Valley streams) 3) river lamprey (Lampetra ayresii); 4) hardhead (Mylopharodon conocephalus); 5) California roach (Hesperoleucus symmetricus); and 6) North American green sturgeon, which is also listed under the ESA. Sacramento splittail (Pogonichthys macrolepidotus), another species of special concern was reported to occur in the Yuba River downstream of Englebright Dam (UC Davis 2012); however YCWA could not find any verified observations of splittail among the referenced studies and reports. Relative abundance, temporal and spatial distribution, and habitat utilization of the reported fish species were derived primarily from two studies conducted between 1986 and 1991, and several ongoing studies that are being conducted by the Yuba River Accord River Management Team (RMT). Chinook salmon was the most abundant species reported among the various studies. During their spawning and rearing periods (September through June), spring-run and fall-run Chinook salmon dominated the numbers of fish observed throughout the Yuba River downstream of Englebright Dam. They accounted for as much as 95 percent of the fish observed in the Rotary Screw Traps (RST) surveys, the snorkel and electrofishing surveys and the VAKI Riverwatcher surveys. 1 In this technical memorandum, fish populations identified under the ESA as evolutionary significant units (ESU) or distinct population segments (DPS) are considered separate species (e.g., Central Valley spring-run Chinook salmon ESU). December 2012 Technical Memorandum 3-9 Non-ESA Fish Below Englebright ©2012, Yuba County Water Agency Page ES-1 Yuba County Water Agency Yuba River Development Project FERC Project No. 2246 YCWA also compared the results of this study with summaries of similar information reported for the lower Feather River, the lower American River, and the lower Tuolumne River. Comparisons of the Yuba River downstream of Englebright Dam species composition with those reported for these other Central Valley tributaries show that the Yuba River downstream of Englebright Dam fish fauna is as diverse as those the other Central Valley stream’s and includes several fish species that, during the recent past, have only been reported in the Yuba River downstream of Englebright Dam (e.g., Chum salmon, pink salmon). Additionally, Yuba River downstream of Englebright Dam includes fish assemblages not found in the lower reaches of these other Central Valley streams (e.g., rainbow trout assemblage). The study was conducted in conformance to the FERC-approved Study 3.9, Non-ESA Listed Fish Populations Downstream of Englebright Dam, with one variance. The FERC-approved study specified the study would be complete by the end of September 2012. The quality assurance/quality control review of study results took longer than anticipated resulting in a slight delay of study completion. The study is complete. Non-ESA Fish Below Englebright Technical Memorandum 3-9 December 2012 Page ES-2 ©2012, Yuba County Water Agency Yuba County Water Agency Yuba River Development Project FERC Project No. 2246 Table of Contents Section No. Description Page No. Executive Summary ...................................................................................................................ES-1 1.0 Goals and Objectives ...........................................................................................................1 2.0 Methods................................................................................................................................1 2.1 Study Area ...............................................................................................................1 2.2 Study Methods .........................................................................................................7 2.2.1 Identify and Acquire Information ................................................................7 2.2.2 Conduct Fish Community Analysis .............................................................7 3.0 Results ..................................................................................................................................8 3.1 Fish Fauna ..............................................................................................................17 3.1.1 Native Fish Assemblages ...........................................................................18 3.1.2 Life History and Status of Fish Species Reported to Occur in the Lower Yuba River......................................................................................19 3.2 Species Composition, Temporal and Spatial Distribution, Relative Abundance and Habitat Utilization ........................................................................52 3.2.1 Fish Species Composition ..........................................................................53 3.2.2 Species Diversity .......................................................................................55 3.2.3 Relative abundance ....................................................................................57 3.2.4 Temporal Distribution ................................................................................64 3.2.5 Spatial Distribution ....................................................................................66 3.2.6 Habitat Utilization ......................................................................................68 3.2.7 Physical Habitat Characterization ..............................................................69 4.0 Discussion ..........................................................................................................................70 5.0 Study-Specific Consultation ..............................................................................................73 5.1 Study-Specific Consultation ..............................................................................................73 6.0 Variances from FERC-Approved Study ............................................................................74 7.0 Attachments to This Technical Memorandum ...................................................................74 8.0 References Cited ................................................................................................................74 List of Figures Figure No. Description Page No. 2.1-1. Lower Yuba River study area, Reach 1(Narrows Reach), from Englebright Dam at RM 24 to the downstream side of the Narrows 1 and Narrows 2 powerhouses at RM 22. .....................................................................................................................3 2.1-2. Lower Yuba River study area, Reach 2 (Garcia Gravel Pit Reach) from Narrows Reach at RM 22 downstream to the USACE’s Daguerre Point Dam near RM 11.5. ................................................................................................................................. 4 December 2012 Technical Memorandum 3-9 Non-ESA Fish Below Englebright ©2012, Yuba County Water Agency Page TOC-i Yuba County Water Agency Yuba River Development Project FERC Project No. 2246 List of Figures (continued) Figure No. Description Page No. 2.1-3. Lower Yuba River study area, Reach 3 (Daguerre Point Dam Reach) from USACE’s Daguerre Point Dam at RM 11.5, downstream to the terminus of the Yuba Goldfield at RM 3.5 extending to the downstream terminus of the Yuba Goldfield at approximately RM 3.5. ....................................................................... 5 2.1-4. Lower Yuba River study area, Reach 4 (Simpson Lane Reach) from Yuba Goldfield at RM 3.5 to the confluence with the Feather River at RM 0