UNITED STATES DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration NATIONAL MARINE FISHERIES SERVICE West Coast Region 650 Capitol Mall, Suite 5-1 00 Sacramento, California 9581 4-4 700 In response refer to: MAY 1 2 2014 WCR-2013-1 Michael J. Farrell Colonel, U.S. Army Commander U.S. Army Engineer District, Sacramento 1325 J Street Sacramento, California 95814-2922 Dear Colonel Farrell: This document transmits NOAA's National Marine Fisheries Service's (NMFS) biological opinion (Enclosure) for the U.S. Army Corps ofEngineers' (Corps) operation and maintenance ofDaguerre Point Dam on the Yuba River. The biological opinion reviews the effects of the action on federally listed threatened Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha), threatened California Central Valley steelhead (0. myldss), the threatened Southern distinct population segment of green sturgeon (Acipenser medirostris), and their designated critical habitat in accordance with section 7(a)(2) of the Endangered Species Act (ESA) of 1973, as amended (16 U.S.C. 1531 et seq.). On August 13, 2013, the U.S. District Court, Eastern District of California, ordered NMFS to file a new biological opinion by May 12, 2014. Your request for reinitiation of formal consultation, which included the final biological assessment, was received on October 22, 2013. The proposed action is the Corps' continued operation and maintenance ofDaguerre Point Dam on the lower Yuba River. Operation and maintenance at Daguerre Point Dam includes operation of the fish ladders (flow gates, baffle boards, debris removal), sediment management, flashboard management, a river stage gage, a contract for operation of fish counting system in the fish ladders and a contract for the installation of flashboards on the dam. The attached document is NMFS' final biological opinion on the Corps' operation and maintenance of existing fish passage facilities at Daguerre Point Dam on the Lower Yuba River, in accordance with section 7 of the ESA. The Corps requested ESA consultation in two separate BAs submitted to NMFS on October 22, 2013: (1) U.S. Army Corps of Engineers Ongoing Operation and Maintenance ofEnglebright Dam and Reservoir on the Yuba River; and 2 (2) U.S. Army Corps of Engineers Authorized Operation and Maintenance of Existing Fish Passage Facilities at Daguerre Point Dam on the Lower Yuba River. It is NMFS understanding that the October 22, 2013, submittal was limited to the Corps' discretionary activities. Effects of the Corps discretionary activities associated with operation and maintenance of Englebright Dam and Englebright Reservoir are addressed in a separate consultation. The attached final biological opinion supersedes the February 29, 2012, NMFS biological opinion on operations of Englebright Dam/Englebright Lake and Daguerre Point Dam on the Yuba River, California. The attached final biological opinion is based on: (1) the biological assessment provided by the Corps on October 22, 2013; (2) key information included in the 2007 Lower Yuba River Fisheries Agreement (Yuba Accord), and 2014 Final Recovery Plan for the Evolutionarily Significant Units ofSacramento River Winter-Run Chinook Salmon and Central Valley Spring-Run Chinook Salmon, and the Distinct Population Segment of Central Valley Steelhead, published by NMFS (2014), and the Yuba Accord Monitoring and Evaluation Program draft interim report (RMT 2013); and (3) scientific literature and reports. A complete administrative record of this consultation is on file at the NMFS, California Central Valley Office. Based on the best available scientific and commercial information, including our review of the biological assessment, this biological opinion concludes that implementation of the proposed action is not likely to jeopardize the above species or adversely modify designated critical habitat. NMFS has included Reasonable and Prudent Measures and discretionary terms and conditions that will minimize incidental take associated with the proposed action. If you have any questions regarding this correspondence please contact Mr. Gary Sprague in our California Central Valley Area Office, 650 Capitol Mall, Suite 5-100, Sacramento, California 95814. Mr. Sprague may be reached by telephone at (916) 930-3615 or by Fax at (916) 930- 3629. Sincerely, /Jlafo~~ ~illiam W. Stelle, Jr. Regional Administrator Enclosure cc: Randy P. Olsen Chief, Operations and Readiness Branch U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, CA 95814 3 Doug Grothe Park Manager Harry L. Englebright Lake U.S. Army Corps of Engineers P.O. Box 6 Smartsville, CA 95977-0006 Lisa H. Clay Senior Assistant District Counsel U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, CA 95814 Copy to File: ARN 151422SWR2013SA00280 Enclosure 1 BIOLOGICAL OPINION ACTION AGENCY: U.S. Army Corps of Engineers ACTION: Operation and Maintenance of Daguerre Point Dam and Fish Ladders CONSULTATION CONDUCTED BY: National Marine Fisheries Service, West Coast Region COVERED SPECIES: Threatened Central Valley spring-run Chinook salmon evolutionarily significant unit (ESU), threatened California Central Valley steelhead distinct population segment (DPS), and threatened Southern DPS of North American green sturgeon CRITICAL HABITAT: Central Valley spring-run Chinook salmon ESU, California Central Valley steelhead DPS, and Southern DPS of North American green sturgeon FILE NUMBER: 151422SVV1t2013SA00280 PCTS TRACKING WCR-2013-1 DATE ISSUED: Contents (I) INTRODUCTION AND BACKGROUND ........................................................................... 1 (A) Environmental Setting ...................................................................................................... 1 (1) Englebright Dam........................................................................................................... 1 (2) Daguerre Point Dam ..................................................................................................... 2 (3) Upper Yuba River ......................................................................................................... 2 (II) CONSULTATION HISTORY ............................................................................................ 2 (A) 2002 Consultation with the Corps on Operations of Englebright Dam and Daguerre Point Dam on the Yuba River, California ................................................................................... 2 (B) 2007 Consultation with the Corps on Operations of Englebright and Daguerre Point Dams on the Yuba River, California ........................................................................................... 3 (C) U. S. District Court, Eastern District of California, 2010 Ruling and 2011/2012 NMFS Consultation with the Corps on Continued Operation and Maintenance of Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir ..................................................................................................................................... 3 (D) 2012 Consultation with the Corps on the Continued Operation and Maintenance of Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir on the Yuba River, California ................................................... 3 (E) Current Consultation ........................................................................................................ 4 (F) 2012 Biological Opinion .................................................................................................. 6 (III) BACKGROUND ................................................................................................................. 6 (A) Section 7 Setting............................................................................................................... 6 (B) ESA Recovery Planning ................................................................................................. 10 (1) California Central Valley Salmonid Recovery Planning ............................................ 10 (C) Lower Yuba River Fisheries Agreement ........................................................................ 11 (D) Hydropower Licensing and Water Deliveries ................................................................ 11 (E) VAKI Riverwatcher Fish Counter.................................................................................. 11 (IV) PROPOSED ACTION (Description of the Proposed Action) ........................................... 11 (A) Proposed Action Components ........................................................................................ 12 (1) Operation and Maintenance of the Fish Passage Facilities at Daguerre Point Dam .. 13 (2) Staff Gage Maintenance ............................................................................................. 19 (3) Administration of a License Issued to CDFW for VAKI Riverwatcher Operations at Daguerre Point Dam ............................................................................................................. 19 i (4) Administration of a License Issued to Cordua Irrigation District for Flashboard Installation, Removal and Maintenance at Daguerre Point Dam .......................................... 19 (5) Protective Conservation Measures ............................................................................. 21 (6) Corps’ Voluntary Conservation Program ..................................................................