COMBINED AQUATICS WORKING GROUP CAWG 13-ANADROMOUS FISH Combined Aquatic Working Group CAWG 13 Anadromous Fish TABLE OF CONTENTS Page Executive Summary..............................................................................................iii 1.0 Introduction .............................................................................................1-1 2.0 Study Implementation .............................................................................2-1 2.1 Study Objectives ..........................................................................2-1 2.2 Study Elements and Implementation............................................2-1 3.0 Methods ..................................................................................................3-1 3.1 General Approach ........................................................................3-1 3.2 Detailed Methods..........................................................................3-1 3.2.1 Review of Information on History, Status and Habitat of Anadromous Salmonids in the SJR Downstream of Friant Dam.........................................................................3-1 3.2.2 Review of Information on Existing and Proposed Projects Including Restoration Programs that may Affect SJR Anadromous Salmonid Populations.................3-2 4.0 Results ....................................................................................................4-1 4.1 History of Anadromous Salmonids in the SJR System.................4-1 4.1.1 Pre 1850 ............................................................................4-1 4.1.2 1850 to 1920......................................................................4-2 4.1.3 1920 to 1940......................................................................4-5 4.1.4 1940-1990..........................................................................4-6 4.1.5 Major Tributaries................................................................4-7 4.2 Status of Anadromous Fish and Their Habitat..............................4-8 4.2.1 Anadromous Salmonid Population Status .........................4-8 4.2.1.1 Steelhead ........................................................4-10 Copyright 2004 by Southern California Edison Company CAWG 13-i Combined Aquatic Working Group CAWG 13 Anadromous Fish 4.2.1.2 Chinook Salmon ..............................................4-10 4.2.2 Current Physical Environmental Conditions.....................4-11 4.2.2.1 Flow .................................................................4-11 4.2.2.2 Channel Morphology and Substrate ................4-13 4.2.2.3 Water Quality...................................................4-14 4.2.3 Current Habitat Conditions...............................................4-20 4.2.3.1 Migration..........................................................4-20 4.2.3.2 Spawning.........................................................4-25 4.2.4 Current Habitat and Population Conditions in the Tributary Streams ............................................................4-30 4.3 Limiting Factors ..........................................................................4-31 4.3.1 Limiting Factors of Anadromous Salmonids Downstream of Friant Dam..............................................4-31 4.3.2 Potential Effects of the Big Creek Project on Anadromous Salmonids Downstream of Friant Dam .......4-34 4.4 Restoration Actions ....................................................................4-36 4.5 Future Programs and Projects....................................................4-38 4.5.1 Increased Water Storage.................................................4-39 4.5.2 Improved Water Quality ...................................................4-44 5.0 Summary.................................................................................................5-1 6.0 Literature Cited........................................................................................6-1 Appendix A. Consultation Documentation Copyright 2004 by Southern California Edison Company CAWG 13-ii Combined Aquatic Working Group CAWG 13 Anadromous Fish EXECUTIVE SUMMARY The purpose of this report is to meet the objectives of the CAWG 13 Anadromous Fish Study Plan (CAWG 13 Study Plan) (SCE 2001) including evaluation of the potential effects (if any) of Big Creek Project operations and maintenance on the anadromous salmonid resources in the San Joaquin River (SJR) downstream of Friant Dam. The study objectives are: 1. Review available information on the history, status and habitat of anadromous salmonids in the San Joaquin River downstream of Friant Dam. 2. Review available information on existing and proposed projects or programs pertaining to the San Joaquin River that may affect anadromous salmonids. 3. Evaluate the effects of operations and maintenance of the Big Creek Projects on anadromous salmonids in the San Joaquin River downstream of Friant Dam. 4. Evaluate the direct, indirect, and cumulative effects of the existing Big Creek Projects and any SCE proposed Project alternatives on anadromous salmonids and their habitat. 5. Evaluate opportunities to benefit anadromous salmonids or their habitat during development and evaluation of any SCE proposed Project alternatives. The general approach used to meet the study objectives included review, summarization, and reporting of information describing the historical and current status of anadromous salmonid populations in the SJR and the potential effects of past, present and foreseeable projects, including habitat restoration. This would be accomplished through completion of five study elements. These study elements are: 1. Review available information to describe status of anadromous salmonids and their habitat in the San Joaquin River downstream of Friant Dam. 2. Identify limiting factors of anadromous salmonids downstream of Friant Dam that may be affected by operations or maintenance of the Big Creek Projects. 3. Review available information that describes other projects, programs, and initiatives in the watershed that may positively or negatively affect anadromous salmonids and their habitats downstream of Friant Dam. Copyright 2004 by Southern California Edison Company CAWG 13-iii Combined Aquatic Working Group CAWG 13 Anadromous Fish This review should consider past, present, and reasonably foreseeable projects. 4. Use information obtained from reviews of existing information and developed from CAWG 12 Water Use and CAWG 6 Hydrology to describe likely direct, indirect, and cumulative effects of the existing SCE Projects and Project alternatives on anadromous salmonids and their habitats. 5. Use existing studies and existing models to evaluate any SCE proposed Project alternatives with other projects, programs, and initiatives in the watershed to minimize Project effects on anadromous salmonids and their habitats. Identify opportunities to benefit anadromous salmonids and their habitats. This report summarizes publicly available information. This report does not present conclusions or evaluations. Evaluations will be included in Study Element 4, which has not yet been implemented, and is described below. The first three study elements have been completed. First, available information describing the status of anadromous salmonids and their habitat in the SJR downstream of Friant Dam was reviewed and summarized in Sections 4.1 and 4.2 of this report. Second, potential limiting factors of anadromous salmonids downstream of Friant Dam were identified in Section 4.3.1. Those limiting factors that may potentially be affected by Big Creek operations were identified in Section 4.3.2. Third, available information that describes other projects, programs, and initiatives in the watershed that may positively or negatively affect anadromous salmonids and their habitats downstream of Friant Dam are reviewed in Sections 4.4 and 4.5 of this report. This review includes past, present, and reasonably foreseeable projects at the time of the preparation of this report. Study elements 4 and 5 have not been implemented at this time. Information developed from the CAWG 6 Hydrology and CAWG 12 Water Use study plans (SCE 2001) will be used to describe likely direct, indirect, and cumulative effects of the existing SCE Projects and Project alternatives on anadromous salmonids and their habitats. Information from Land-3 Cumulative Effects Analysis also will be used for this description. Secondly, existing studies and existing models will be used to evaluate any SCE proposed Project alternatives with other projects, programs, and initiatives in the watershed to minimize Project effects on anadromous salmonids and their habitats. Opportunities to benefit anadromous salmonids and their habitats will be identified. Information included in the protection, mitigation, and enhancement measures (PM&E) phase of the Big Creek Alternative Licensing Process (ALP), as well as CAWG 6 Hydrology and CAWG 12 Water Use reports may be used to assist in implementation of this study element. Copyright 2004 by Southern California Edison Company CAWG 13-iv Combined Aquatic Working Group CAWG 13 Anadromous Fish Historically, the SJR supported what was reportedly one of the largest, spring-run Chinook salmon population in North America. Fall-run Chinook salmon and steelhead trout also were present. During the past 150 years, however, spring- run Chinook salmon have been extirpated and fall-run Chinook salmon and steelhead now only occur in the lower reaches of the SJR’s three major tributaries, the Stanislaus,