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Assessment of Fish Migration at Riffles in Sunol Valley Quarry Reach of Alameda Creek

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Assessment of Fish Migration at Riffles in Sunol Valley Quarry Reach of Alameda Creek TECHNICAL MEMORANDUM ASSESSMENT OF FISH MIGRATION AT RIFFLES IN SUNOL VALLEY QUARRY REACH OF ALAMEDA CREEK Prepared for San Francisco Public Utilities Commission February 2010 Table of Contents TABLE OF CONTENTS 1 INTRODUCTION .............................................................................................................................. 1-1 1.1 BACKGROUND INFORMATION ...................................................................................... 1-1 1.2 PURPOSE.............................................................................................................................. 1-1 1.3 SCOPE................................................................................................................................... 1-1 1.4 ORGANIZATION OF TECHNICAL MEMORANDUM .................................................... 1-2 2 SETTING............................................................................................................................................ 2-1 2.1 ALAMEDA CREEK IN THE SUNOL VALLEY ................................................................ 2-1 2.2 STUDY AREA ......................................................................................................................2-6 2.3 ONGOING STUDIES AND ACTIONS ............................................................................... 2-6 3 METHODS ......................................................................................................................................... 3-1 3.1 RIFFLE TRANSECT SURVEYS ......................................................................................... 3-1 3.1.1 Entrix 2004 Surveys .............................................................................................. 3-1 3.1.2 HDR|SWRI 2006 Surveys..................................................................................... 3-3 3.2 RIFFLE PASSAGE CRITERIA............................................................................................ 3-3 3.3 DATA ANALYSIS................................................................................................................ 3-4 3.3.1 Development of Rating Curves ............................................................................. 3-4 3.3.2 Estimation of Passage Flow................................................................................... 3-6 4 RESULTS ........................................................................................................................................... 4-1 4.1 2006 SURVEY OBSERVATIONS ....................................................................................... 4-1 4.2 STEELHEAD MIGRATION FLOWS .................................................................................. 4-6 4.2.1 Riffle XS1.............................................................................................................. 4-8 4.2.2 Riffle CP7.............................................................................................................. 4-9 4.2.3 Riffle XS4............................................................................................................ 4-10 4.2.4 Riffle XS3............................................................................................................ 4-11 4.2.5 Riffle XS2............................................................................................................ 4-12 4.2.6 Riffle CP6............................................................................................................ 4-13 4.2.7 Riffle CP5............................................................................................................ 4-14 4.2.8 Riffle CP4-2 ........................................................................................................ 4-16 4.2.9 Riffle CP4-1 ........................................................................................................ 4-17 4.2.10 Riffle CP3............................................................................................................ 4-18 5 DISCUSSION..................................................................................................................................... 5-1 5.1 STUDY LIMITATIONS ....................................................................................................... 5-2 5.1.1 Identification of Controlling Riffle ....................................................................... 5-2 5.1.2 Limitations of Passage Flow Estimates................................................................. 5-2 5.2 RESULTS IN CONTEXT OF RECHARGE, ACCRETION, AND MODIFICATION ....... 5-3 5.2.1 Passage Flow Estimates in Context of Flow Losses and Accretion ...................... 5-3 5.2.2 Passage Flow Estimates in Context of Planned Modifications ............................. 5-3 6 CONCLUSION................................................................................................................................... 6-1 7 REPORT PREPARATION................................................................................................................. 7-1 7.1 LIST OF PREPARERS ......................................................................................................... 7-1 7.2 ACKNOWLEDGMENTS ..................................................................................................... 7-1 8 REFERENCES ................................................................................................................................... 8-1 Riffles February 2010 Page i Assessment of Fish Upstream Migration at Riffles in Sunol Valley Quarry Reach of Alameda Creek Figures Figure 2-1 Study Area and Vicinity Figure 2-2 Flow at Alameda Creek below Welch Creek (Water Years 2000 to 2008) Figure 2-3 Current and Historical Alignment of Alameda Creek Figure 2-4 Elevation Profile of Alameda Creek in the Sunol Valley Figure 3-1 Example Stage versus Discharge (Rating Curve) Relationship Developed from Available Flow Measurements Figure 3-2 Example of an Estimate of Adult Passage Water Surface Elevation Figure 3-3 Minimum Flow Calculations for Adult and Juvenile Passage at a Hypothetical Riffle Location Figure 4-1 Approximate Cross Section Locations Figure 4-2 Riffle just Upstream of where Calaveras Road Crosses Alameda Creek (XS1) Figure 4-3 Riffle at the Bridge over Alameda Creek near the Sunol Valley Water Treatment Plant Figure 4-4 Riffle Approximately 0.5 mile Downstream of the Bridge Near the Sunol Valley Water Treatment Plant Figure 4-5 Subsurface Flow Location on Alameda Creek Figure 4-6 Concrete Structures with Potential to Limit Migration at Low Flows Figure 4-7 Typical Channel Geomorphology in the Vicinity of Riffles XS4, XS3, and XS2 Figure 4-8 Passage Water Surface Elevations at Riffle XS1 Figure 4-9 Stage-Discharge Relationship for Riffle XS1 Figure 4-10 Passage Water Surface Elevations at Riffle CP7 Figure 4-11 Stage-Discharge Relationship for Riffle CP7 Figure 4-12 Passage Water Surface Elevations at Riffle XS4 Figure 4-13 Stage-Discharge Relationship for Riffle XS4 Figure 4-14 Passage Water Surface Elevations at Riffle XS3 Figure 4-15 Stage Discharge Relationship for Riffle XS3 Figure 4-16 Passage Water Surface Elevations at Riffle XS2 Figure 4-17 Stage Discharge Relationship for Riffle XS2 Figure 4-18 Passage Water Surface Elevations at Riffle CP6 Figure 4-19 Stage-Discharge Relationship for Riffle CP6 Figure 4-20 Observed Water Surface Elevations at Riffle CP5 Figure 4-21 Passage Water Surface Elevations at Riffle CP5 Figure 4-22 Stage-Discharge Relationship for the Right Side of Riffle CP5 Figure 4-23 Passage Water Surface Elevations at Riffle CP4-2 Figure 4-24 Stage-Discharge Relationship for Riffle CP4-2 Figure 4-25 Passage Water Surface Elevations at Riffle CP4-1 Figure 4-26 Stage-Discharge Relationship for Riffle CP4-1 Figure 4-27 Passage Water Surface Elevations at Riffle CP3 Figure 4-28 Stage-Discharge Relationship for Riffle CP3 Figure 5-1 PG&E Pipeline Concrete Apron Drop Structure Riffles February 2010 Page ii Table of Contents Tables Table 2-1 Approximate Acreage Within the Alameda Creek Watershed, its Three Sub- Watersheds, and the Five Basins in the Upper Alameda Creek Sub-Watershed Table 3-1 Summary of Flow Data Used to Develop Stage versus Discharge Relationships at Riffles Surveyed in 2004 Table 3-2 Steelhead Passage Element Timing Table 4-1 Estimated Minimum Flows to Support Steelhead Migration Table 4-2 Summary of Flow Data Used to Develop Stage versus Discharge Relationships at Subject Riffles Surveyed in 2006 Riffles February 2010 Page iii Assessment of Fish Upstream Migration at Riffles in Sunol Valley Quarry Reach of Alameda Creek List of Acronyms BART Bay Area Rapid Transit CDFG California Department of Fish and Game cfs cubic feet per second CP subject riffles surveyed in 2004 fps feet per second HDR|SWRI HDR Engineering, Inc.|Surface Water Resources, Inc. I-680 Interstate 680 NMFS National Marine Fisheries Service PG&E Pacific Gas and Electric Company SFPUC San Francisco Public Utilities Commission SVQR Sunol Valley quarry reach (of Alameda Creek) TAC Technical Advisory Committee URS URS Corporation USGS U.S. Geological Survey WSE water surface elevation XS subject riffles surveyed in 2006 Riffles February 2010 Page iv 1.0 Introduction 1 INTRODUCTION 1.1 BACKGROUND INFORMATION The San Francisco Public Utilities Commission (SFPUC) has been working with other stakeholders since the late 1980s to restore steelhead (Oncorhynchus mykiss) to the Alameda Creek Watershed (TAC, 1989). In
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