Final Environmental Assessment/Initial Study: Authorization of Incidental Take and Implementation of the Calaveras River Habitat Conservation Plan Prepared By: Stockton East Water District and The National Oceanic and Atmospheric Administration National Marine Fisheries Service August 2020 Calaveras River HCP FINAL EA/IS Executive Summary In accordance with the National Environmental Policy Act (NEPA), the National Oceanic and Atmospheric Administration National Marine Fisheries Service (NMFS) has developed this Environmental Assessment/Initial Study (EA/IS) to evaluate the effects of the proposed action of issuing an Incidental Take Permit (ITP) under Section 10(a)(1)(B) of the Endangered Species Act (ESA) of 1973, as amended, to Stockton East Water District (District or the applicant) related to the District’s Calaveras River Operations (Project). The District is applying to NMFS for an ITP for a 50-year period authorizing the incidental take of threatened Central Valley (CV) steelhead (Oncorhynchus mykiss) Distinct Population Segment (DPS), threatened CV spring-run Chinook salmon (O. tshawytscha) Evolutionarily Significant Unit (ESU), endangered Sacramento River winter-run Chinook salmon ESU, and species of special concern CV fall/late fall-run Chinook salmon ESU. As a species of special concern, the fall/late fall-run Chinook salmon ESU does not currently have any protective regulations against take and no Federal permit is needed to incidentally take them, but there may be a change in listing status during the permit period. As such, the ITP authorization would be effective immediately upon issuance for all threatened and endangered species (i.e., CCV steelhead DPS, CV spring-run Chinook salmon ESU, and Sacramento River winter-run Chinook salmon ESU); while the ITP authorization would become effective for the fall/late fall-run Chinook salmon ESU if it is listed as threatened or endangered. On September 30, 2019, NMFS published a notice of receipt in the Federal Register (84 FR 51518) that a request for a permit for the incidental take of winter-run Chinook salmon, spring-run Chinook salmon, fall/late fall-run Chinook salmon, and CCV steelhead associated with the activities as described in the Habitat Conservation Plan, had been submitted by the District. A draft version of this EA/IS was made available for a 45- day public comment period. NMFS received several comments and these comments were addressed as changes to this Final EA/IS or as a response to comments in section 9 below. NMFS’ issuance of the ITP is contingent on the District’s implementation of the Calaveras River Habitat Conservation Plan (CHCP), which was developed in coordination with NMFS (FISHBIO et al. 2018). The District has developed and will implement the CHCP to ensure that the ongoing management and operation of the Project is coordinated with the needs of Calaveras River salmonid populations and to meet the issuance criteria for an ITP. Under the CHCP, the District will continue to function as a regional water supplier, and will retain the ongoing operation and maintenance of existing structures and facilities in the lower Calaveras River corridor, in some instances modified to provide fish protection. The CHCP includes a series of conservation strategies (CS) to minimize and mitigate the effects of Project operations on potential take of listed steelhead and Chinook salmon. This EA/IS analyzes a permit term of 50 years, assuming initial permit issuance would occur in 2019. The conclusion from the evaluation of this EA/IS is that the Proposed Action will not result in any significant adverse direct, indirect, or cumulative impacts to the human environment. i Calaveras River HCP FINAL EA/IS Table of Contents EXECUTIVE SUMMARY ............................................................................................................... i 1.0 INTRODUCTION ................................................................................................................ 1 2.0 PURPOSE AND NEED ........................................................................................................ 4 3.0 DESCRIPTION OF PROPOSED ACTION AND ALTERNATIVES ................................. 4 3.1 NO ACTION ALTERNATIVE .................................................................................... 4 3.2 PROPOSED ACTION .................................................................................................. 6 3.2.1 Covered Activities .............................................................................................. 6 3.2.2 Conservation Program ........................................................................................ 8 3.3 CONSERVATION STRATEGIES/MITIGATION MEASURES ................................. 8 3.3.1 Conservation Strategies for New Hogan Reservoir Water Impoundment and Non-flood Control Operations (OM1) ................................................................ 19 3.3.2 Conservation Strategies for SEWD Old Calaveras River Headworks Facility Operations (OM2) ............................................................................................... 40 3.3.3 Conservation Strategies for SEWD Bellota Diversion Facility Operations (OM3) ................................................................................................................. 42 3.3.4 Conservation Strategies for Artificial Instream Structures and SEWD Small Instream Operations (OM4) ................................................................................ 47 3.3.5 Conservation Strategies for Privately Owned Diversion Facilities Operated within the District’s Service Areas (OM5) ......................................................... 55 3.3.6 Conservation Strategies for SEWD Channel Maintenance for Instream Structures (OM6) ................................................................................................ 57 3.3.7 Conservation Strategies for Fisheries Monitoring Program (OM7) ................. 58 3.4 CONSTRUCTION ACTIVITIES ................................................................................. 59 3.5 ALTERNATIVES CONSIDERED BUT DISMISSED FROM FURTHER ANALYSIS ................................................................................................................. 61 3.5.1 Flashboard Dams installed later than April 15 ................................................. 61 3.5.2 Artificial adult O. mykiss and Chinook migration flows ................................. 62 3.5.3 Artificial juvenile O. mykiss and Chinook migration pulse flows ................... 64 3.5.4 Moving the SEWD Intake from Bellota to a location closer to the Dr. Joe Waidhofer Water Treatment Plant ...................................................................... 67 3.5.5. Reduced Permit Term (25 years) ..................................................................... 67 4.0 AFFECTED ENVIRONMENT .......................................................................................... 68 4.1 AGRICULTURAL RESOURCES ............................................................................. 71 4.2 AIR QUALITY ........................................................................................................... 72 4.3 CULTURAL AND HISTORICAL RESOURCES ..................................................... 73 4.4 GEOLOGY, SOILS, AND SEISMICITY .................................................................. 74 4.5 BIOLOGICAL RESOURCES .................................................................................... 75 4.6 HAZARDOUS & TOXIC MATERIALS .................................................................. 97 4.7 HYDROLOGY AND WATER QUALITY ................................................................ 98 4.8 RECREATION ......................................................................................................... 101 4.9 TRANSPORTATION ............................................................................................... 103 5.0 ENVIRONMENTAL CONSEQUENCES ....................................................................... 103 5.1 ENVIRONMENTAL ISSUES DISMISSED FROM DETAILED ANALYSIS ...... 107 5.1.1 Aesthetics ................................................................................................... 107 5.1.2 Land Use Planning ..................................................................................... 107 5.1.3 Mineral Resources ...................................................................................... 108 5.1.4 Noise .......................................................................................................... 108 5.1.5 Population Growth and Housing ................................................................ 108 ii Calaveras River HCP FINAL EA/IS 5.1.6 Public Health and Hazards ......................................................................... 109 5.1.7 Public Service and Utilities ........................................................................ 109 5.1.8 Socioeconomics.......................................................................................... 109 5.1.9 Environmental Justice ................................................................................ 109 5.1.10 Indian Trust Assets ..................................................................................... 110 5.2 EFFECTS FROM NO ACTION ALTERNATIVE .................................................. 110 5.2.1 Agricultural Resources ............................................................................... 110 5.2.2 Air Quality ................................................................................................