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1 UNITED STATES OEPARTMENT OF COMMERCE NATIONAL Oceanic and Atmospheric Administration NATIONAL MARINE FISHERIES SERVICE Southwest Region 501 West Ocean Boulevard, Suite 4200 Long Beach, California 90802-421 3 MV B $ In response refer to: F/S WR/2003/02258 Michael Finan Chief, Delta Office Army Corps of Engineers 1325 J Street Sacramento, California 958 14-2922 Dear Mr. Finan: This letter transmits NOAA's NATIONAL MARINE FISHERIES SERVICE 's (NMFS) biological opinion (Enclosure 1) based on our review of the City of Stockton Delta Water Supply project (DWSP) in San Joaquin County, California , and its effects on Federally listed endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), threatened Central Valley spring-run Chinook salmon (0. tshawytscha), threatened Central Valley steelhead (0. mykiss), threatened southern distinct population segment of North American green sturgeon (Acipenser medirostris), and designated critical habitat for Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, and Central Valley steelhead in accordance with section 7 of the Endangered Species Act (ESA) of 1973, as amended (16 1531 et seq.)

2 Your initial request for section 7 consultation on this project was received on November 17,2004. Subsequently, in January 2005, consultation was suspended when additional sites and fish screen designs were added to the project description. At an April 25,2005, meeting involving representatives of the applicant ( , the City of Stockton), NMFS, the Fish and Wildlife SERVICE and the California Department of Fish and Game, NMFS staff requested that a single project alternative be chosen before further formal consultation could continue. NMFS received additional information from the applicant describing the project's operations and effects in a Draft Program Environmental Impact Report (PEIR) on April 29,2005, a final PEIR on October 26,2005, and a final biological assessment on February 28,2006, in which a final project alternative was selected.

3 NMFS sent a letter informing the Army Corps of Engineers (Corps) that formal consultation for the DWSP was initiated with the receipt of the February 28,2006, final biological assessment. This biological opinion is based on information provided in the April 29,2005, draft PEIR, October 26,2005, final PEIR, and the February 28,2006, final biological assessment; and, numerous scientific articles and reports from both the peer reviewed literature and agency "gray literature." A complete administrative record of this consultation is on file at the Sacramento Area Office of hTMFS. STKN-15 Based on the best available scientific and commercial information, the biological opinion concludes that the City of Stockton DWSP, as presented by the Corps and the applicant, is not likely to jeopardize the continued existence of the listed species, or destroy or adversely modify designated critical habitat.

4 NMFS also has included an incidental take statement with reasonable and prudent measures and non-discretionary terms and conditions that are necessary and appropriate to avoid, minimize, or monitor incidental take associated with the project of listed salmonids. The section 9 prohibitions against taking of listed species and the terms and conditions of this biological opinion will not apply to North American green sturgeon until the final section 4(d) ruling under the ESA has been published in the Federal Register. This letter also transmits NMFS' Essential Fish Habitat (EFH) conservation recommendations for Pacific salmon (0. tshawytscha) and Pacific Coast groundfish as required by the Magnuson-Stevens Fishery Conservation and Management Act (MSA), as amended (16 1801 et seq.; Enclosure 2). The document concludes that the City of Stockton DWSP will adversely affect the EFH of Pacific salmon in the action area and adopts certain terms and conditions of the incidental take statement and the ESA conservation recommendations of the biological opinion as the EFH conservation recommendations.

5 The Corps has a statutory requirement under section 305(b)(4)(B) of the MSA to submit a detailed response in writing to NMFS within 30 days of receipt of these conservation recommendations that includes a description of the measures proposed for avoiding, mitigating, or offsetting the impact of the activity on EFH (50 CFR a)). If unable to complete a final response within 30 days, the Corps should provide an interim written response within 30 days before submitting its final response. Please contact Mr. Jeffrey Stuart in our Sacramento Area Office at (916) 930-3607 or via e-mail at if you have any questions regarding this response or require additional information. Sincerely, odney R. McInnis Administrator Enclosures (2) 1. Biological Opinion with appendices 2. Essential Fish Habitat Conservation Recommendations cc: Copy to file-ARN# 15 1422s WR2005SA9037 James Starr, California Department of Fish and Game, 4001 North Wilson Way, Stockton, CA 94205 STKN-15 Ryan Olah, Fish and Wildlife SERVICE , 2800 Cottage Way, Room W-2605, Sacramento, CA 95825 Robert Granberg, Deputy Director, Water Resources Planning, Department of Municipal Utilities, City of Stockton, 2500 Navy Drive, Stockton, CA 95206-1 191 STKN-15 BIOLOGICAL OPINION ACTION AGENCY: Army Corps of Engineers, Sacramento District ACTIVITY: Construction and Operation of the City of Stoclton Delta Water Supply Project CONSULTATION CONDUCTED BY: NOAA's NATIONAL MARINE FISHERIES SERVICE , Southwest Region FILE NUMBER: 200310225 8 DATE ISSUED: NQV 2 9 2008 I.

6 CONSULTATION HISTORY On November 6, 2003, staff from the NATIONAL MARINE FISHERIES SERVICE (NMFS) attended an interagency pre-application meeting with the Army Corps of Engineers (Corps) to discuss the City of Stockton Delta Water Supply project (DWSP) and its potential effects upon listed species under the Endangered Species Act (ESA). In attendance were representatives of the City of Stockton (City), their consultants (Environmental Science Associates [Associates]) and the Environmental Protection Agency (EPA). On November 13,2003, the Notice of Preparation for the DWSP was mailed to these agencies by the City. On January 23,2004, NMFS provided a list of protected anadromous salmonids potentially found within the actionarea to the City's environmental consultants. On May 21 and June 8,2004, representatives of the City met with staff from NMFS and the California Department of Fish and Game (CDFG) to discuss the design of the DWSP intake structure as well as fish screen requirements.

7 On November 17,2004, the Corps initiated formal consultation with NMFS on the DWSP. The project description included two alternative fish screen designs: (1) an in-bank slanted fish screen, or (2) an in-channel vertical fish screen design located on the northern bank of the San Joaquin River at the southwest corner of Empire Tract. On December 13, 2004, NMFS responded to the Corps with a letter indicating that formal consultation had been initiated on the project, and that the analysis would look at both types of fish screen placements described in the project description. In January 2005, NMFS was informed by the Corps that the City had modified its project description and was considering an alternative project site located on the western side of Empire STKN-15project, none of which was designated as the preferred alternative.

8 NMFS requested verbally that the Corps suspend its consultation until a final alternative was selected for the project design by the City of Stockton. On April 25, 2005, representatives of the City met with staff from NMFS, Fish and Wildlife SERVICE (FWS), and CDFG to discuss the DWSP biological assessment previously submitted to the agencies by the Corps. At that meeting, NMFS requested that the biological assessment (BA) be resubmitted with only one alternative for the proposed project rather than several alternatives. The Draft Program Environmental Impact Report (PEIR) (Associates 2005) was mailed to NMFS, FWS, and CDFG on April 29, 2005. This document contained the four design alternatives first identified in January 2005. The Final PEIR was mailed to NMFS, FWS, and CDFG on October 26, 2005. In this document, the design alternatives had been reduced to the original two fish screen designs at the San Joaquin River location originally described.

9 On February 28, 2006, NMFS received the final BA from the Corps (Associates 2006) which described the final project design for the selected alternative. The preferred project was the in-bank fish screen design on the northern bank of the San Joaquin River at the southwest tip of Empire Tract. On March 27, 2006, NMFS responded in writing to the Corps that formal consultation for the DWSP was initiated with the receipt of the February 28, 2006, final BA. II. DESCRIPTION OF THE PROPOSED ACTION The DWSP is designed as a conjunctive use water supply program for the City of Stockton Metropolitan Area (COSMA), which would integrate surface water and ground water management under one program. The surface water component of the DWSP would include a new screened intake facility on the San Joaquin River, new pipelines to convey Delta water to a new water treatment plant (WTP) located just north of the COSMA, and new treated water pipelines to deliver water to the City s existing water distribution system.

10 Existing interties with the California Water SERVICE Company (Cal Water) would be used to distribute the DWSP s treated water throughout Cal Water s SERVICE area within the COSMA. The groundwater component would include coordinated groundwater and surface water management. Initially, groundwater levels would be allowed to recover by in-lieu (natural) recharge. Ultimately, treated Delta surface water would be injected into the groundwater basin underlying the COSMA, for later extraction during periods of limited surface water supply. The DWSP would be expanded incrementally to keep pace with the COSMA s needs, based on the timing of existing supply reductions and increased demand over time. The initial capacity of the DWSP would be 30 million gallons per day (mgd) (47 cubic feet per second (cfs)), with staged incremental expansions to an ultimate capacity of 160 mgd (250 cfs).