California Department of Fish and Wildlife Ecosystem Conservation Division P.O. BOX 944209 SACRAMENTO, CA, 94244-2090 California Endangered Species Act Incidental Take Permit No. 2081-2019-066-00 LONG-TERM OPERATION OF THE STATE WATER PROJECT IN THE SACRAMENTO SAN JOAQUIN DELTA Authority: This California Endangered Species Act (CESA) incidental take permit (ITP) is issued by the California Department of Fish and Wildlife (CDFW) pursuant to Fish and Game Code section 2081, subdivisions (b) and (c), and California Code of Regulations, Title 14, section 783.0 et seq. CESA prohibits the take1 of any species of wildlife designated by the California Fish and Game Commission as an endangered, threatened, or candidate species.2 CDFW may authorize the take of any such species by permit if the conditions set forth in Fish and Game Code section 2081, subdivisions (b) and (c) are met. (See Cal. Code Regs., tit. 14, § 783.4). Permittee: California Department of Water Resources Principal Officer: Michelle Banonis, Assistant Chief Deputy Director Contact Person: Dean Messer, 916-376-9700 Mailing Address: P.O. Box 942836 Sacramento, CA 94236-0001 Effective Date and Expiration Date of this ITP: This ITP shall be executed in duplicate original form and shall become effective once a duplicate original is acknowledged by signature of the Permittee on the last page of this ITP and returned to CDFW’s Habitat Conservation Planning Branch at the address listed in the Notices section of this ITP. Unless renewed by CDFW, this ITP’s authorization to take the Covered Species shall expire on March 31, 2030. 1Pursuant to Fish and Game Code section 86, “‘take’ means hunt, pursue, catch, capture, or kill, or attempt to hunt, pursue, catch, capture, or kill.” (See also Environmental Protection Information Center v. California Department of Forestry and Fire Protection (2008) 44 Cal.4th 459, 507 [for purposes of incidental take permitting under Fish and Game Code section 2081, subdivision (b), “‘take’ … means to catch, capture or kill”.) 2The definition of an endangered, threatened, and candidate species for purposes of CESA are found in Fish and Game Code sections 2062, 2067, and 2068, respectively. Notwithstanding the expiration date on the take authorization provided by this ITP, Permittee’s obligations pursuant to this ITP do not end until CDFW accepts as complete the Permittee’s Final Mitigation Report required by Condition of Approval 7.3 of this ITP. Project Location: The Long-Term Operation of the State Water Project (Project) is located within the following geographic area (Project Area, See Figures 1A and B): • Sacramento River from its confluence with the Feather River downstream to the legal Delta boundary at the I Street Bridge in the City of Sacramento; • Sacramento-San Joaquin Delta (i.e., upstream to Vernalis and downstream to Chipps Island); and • Suisun Marsh and Bay Project operations will be in all fish-bearing waterways within the Project Area. The northern edge of the Project Area is located approximately 8.56 km northeast of Knights Landing in Yolo County at approximately 38.785281 latitude, -121.621825 longitude and extends downstream on the Sacramento River to the Sacramento-San Joaquin Delta (Delta). To the south and east the Project Area is bounded by the legal boundary of the Delta. To the west the Project Area is bounded by the legal Delta, Suisun Marsh, and Suisun Bay. Project Description: This Project Description is based on information CDFW obtained from Permittee’s December 2019 ITP application and subsequent coordination with Permittee. The Conditions of Approval begin on page 49. 1. Introduction The State Water Project (SWP) includes water, power, and conveyance systems, conveying an annual average of 2.9 million acre-feet (AF) of water. The principal facilities of the SWP are Oroville Reservoir and related facilities, and San Luis Dam and related Incidental Take Permit No. 2081-2019-066-00 CALIFORNIA DEPARTMENT OF WATER RESOURCES LONG TERM OPERATION OF THE STATE WATER PROJECT IN THE SACRAMENTO-SAN JOAQUIN DELTA Page 2 facilities, facilities in the Delta, the Suisun Marsh Salinity Control Gates (SMSCG), the California Aqueduct including its terminal reservoirs and the Delta-Mendota Canal/California Aqueduct Intertie (DCI), and the North and South Bay Aqueducts. Permittee holds contracts with 29 public agencies in northern, central, and southern California for water supplies from the SWP. Water stored in the Oroville facilities, along with water available in the Delta (consistent with applicable regulations) is captured in the Delta and conveyed through several facilities to SWP contractors. The SWP is operated to provide flood control and water for agricultural, municipal, industrial, recreational, and environmental purposes. 1.1 Description of Existing SWP Facilities The SWP facilities in the Delta provide for delivery of water supply to areas within and immediately adjacent to the Delta, and to regions south of the Delta. The SWP Delta facilities include the Suisun Marsh and Bay facilities, the Harvey O. Banks Pumping Plant (Banks Pumping Plant), the Clifton Court Forebay (CCF), the John E. Skinner Delta Fish Protective Facility, and the Barker Slough Pumping Plant (BSPP). 1.1.1 Harvey O. Banks Pumping Plant The Harvey O. Banks Pumping Plant (Banks Pumping Plant), located about 12.87 km northwest of Tracy, marks the upstream end of the California Aqueduct. The plant discharges into five pipelines that convey water into a roughly 1.6 km- long canal, which in turn conveys water to Bethany Reservoir.3 The Banks Pumping Plant consists of 11 pumps—two rated at 375 cubic feet per second (cfs) capacity, five at 1,130 cfs capacity, and four at 1,067 cfs capacity—that provide the initial lift of water 74.37 m from the CCF into the California Aqueduct. The rated capacity of the Banks Pumping Plant is 10,300 cfs. The plant’s maximum daily pumping rate is controlled by a combination of the State Water Resources Control Board’s (SWRCB’s) Water Rights Decision 1641 (D-1641) and permits 3 DWR and Reclamation (2015). Technical Information for Preparing Water Transfer Proposals. Information for Parties Preparing Proposals for Water Transfers Requiring Department of Water Resources or Bureau of Reclamation Approval. Incidental Take Permit No. 2081-2019-066-00 CALIFORNIA DEPARTMENT OF WATER RESOURCES LONG TERM OPERATION OF THE STATE WATER PROJECT IN THE SACRAMENTO-SAN JOAQUIN DELTA Page 3 issued by the United States Army Corps of Engineers (USACE) that regulate the rate of diversion of water into the CCF. The diversion rate is normally restricted to 6,680 cfs as a three-day average inflow and 6,993 cfs as a 1-day average inflow to the CCF in accordance with the existing USACE Section 10 permit issued pursuant to the Rivers and Harbors Act.4 The diversions may be greater in the winter and spring, depending on San Joaquin River flows at Vernalis.3 As part of the adaptive management process described in D-1641, the SWP is permitted to pump an additional 500 cfs between July 1 and September 30 to offset water costs associated with fisheries actions, making the summer limit effectively 7,180 cfs.5 The U.S. Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP). The CVP regularly uses the SWP facilities through 1) direct export at Banks Pumping Plant using Joint Point of Diversion (JPOD) provisions in D-1641, or 2) through the use of the DCI and pumping water directly into the California Aqueduct (CA) for conveyance to CVP storage and water users. 1.1.2 John E. Skinner Delta Fish Protective Facility The John E. Skinner Delta Fish Facility (Skinner Fish Facility) is west of the CCF, about 3.22 km upstream from the Banks Pumping Plant. The Skinner Fish Facility guides fish away from entering the pumps that convey water into the CA. Large fish and debris are directed away from the facility by a 118-meter-long trash boom. Smaller fish are diverted from the intake channel into bypasses by a series of metal louvers. These smaller fish pass through a secondary system of screens, louvers, and pipes into seven holding tanks, where a subsample is counted and recorded. The salvaged fish are then returned to the Delta in oxygenated tank trucks. 4 State Water Resources Control Board. 2017. Scientific Basis Report in Support of New and Modified Requirements for Inflows from the Sacramento River and its Tributaries and Eastside Tributaries to the Delta, Delta Outflows, Cold Water Habitat, and Interior Delta Flows. 5 U.S. Bureau of Reclamation. 2008. Biological Assessment on the Continued Long-Term Operations of the Central Valley Project and the State Water Project. Mid-Pacific Region, Sacramento, CA. August 2008. Incidental Take Permit No. 2081-2019-066-00 CALIFORNIA DEPARTMENT OF WATER RESOURCES LONG TERM OPERATION OF THE STATE WATER PROJECT IN THE SACRAMENTO-SAN JOAQUIN DELTA Page 4 During normal operations, salvaged fish are transported approximately 30 km and released at one of six SWP and CVP release sites near the confluence of the Sacramento and San Joaquin Rivers. Up to present day, most fish hauls from the Skinner Fish Facility and the CVP Tracy Fish Facility have been released at either the SWP Horseshoe Bend Release Site or the SWP Curtis Landing Release Site on an alternating basis. In 2018, two new SWP release sites were constructed on Sherman Island (SWP Little Baja and SWP Manzo Ranch), and as a measure to reduce predation, Permittee plans to re-operate the release site rotation schedule to incorporate the two new release sites, the two CVP release sites at Emmaton and Antioch, and the SWP Curtis Landing Release Site. The SWP Horseshoe Bend Release Site is planned to be decommissioned from regular use due to age and lack of interagency operability.