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South Bay Salt Ponds Initial Stewardship Plan June 2003

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South Bay Salt Ponds Initial Stewardship Plan June 2003 South Bay Salt Ponds Initial Stewardship Plan June 2003 Prepared by: Submitted by: US Fish and Wildlife CA Dept of Service Fish and Game Table of Contents Responsible Parties California Department of Fish and Game 7329 Silverado Trail Yountville, CA 94599 (707) 944-5525 Contact: Carl Wilcox, Environmental Services Supervisor US Fish and Wildlife Service San Francisco Bay Wildlife Refuge Complex PO Box 524 Newark, CA 94560 (510) 792-0222 Contact: Marge Kolar Initial Stewardship Plan Preparation Life Science!, Inc. 1059 Court St, #106 Woodland, CA 95695 (530) 668-5667 lifescienceinc.com Contact: Lisa Stallings, Ph.D. Project Manager. Leslie Allen, Project Assistant Technical Support, Document Preparation, and Graphics were provided by the following: Rachel Bonnefil, Acta Environmental Ed Gross, Schaaf and Wheeler Nancy Kang Tom Lagerquist, Peregrine Environmental Roger Levanthal, FarWest Restoration Engineering Doug Lipton, Ph.D., Lipton Environmental Group David Markham, Ph.D. Dan Schaaf, Schaaf and Wheeler Kirk Wheeler, Schaaf and Wheeler i Table of Contents ii Table of Contents Table of Contents 1.0 Project Overview 1.1 Context………………………………………………………………………………………….1 - 1 1.2 Location of Project………………………………………………………………..……………1 - 2 1.2.1 Baumberg Complex…………………………………………………………………………1- 4 1.2.2 Alviso Complex, including Alviso Ponds………………………………………. ………...1 - 6 1.2.3 West Bay Pond Complex…………………………………………………………………...1 - 8 1.3 Site Background and History………………………………………………………………… 1 - 10 2.0 Environmental Setting 2.1 Biological Resources……………………………………………………………………………2 - 1 2.1.1 Vegetation………………………………………………………………………………….. 2 - 1 2.1.1.2 Vegetation within Salt Ponds……………………………………………………………….. 2 - 2 2.1.1.3 Vegetation along Sloughs and Creeks………………………………………………………… 2 - 3 2.1.2 Wildlife……………………………………………………………………………………,,..2 - 3 2.1.2.1 Waterfowl ………………………………………………………………………………...…2 - 4 2.1.2.2 Shorebirds …………………………………………………………………………………. 2 - 4 2.1.2.3 Other Bird Species ………..………………………………………………………………...2 - 5 2.1.2.4 Fish ………………………………………………………………………………………....2 - 6 2.1.2.5 Special Status Species ........................................................................................................... 2 - 7 2.1.2.6 Listed Species.......................................................................................................................... 2 - 12 2.1.2.7 Non-listed Species.............................................................................................................. 2 - 15 2.1.2.8 Special Status Fish Species.................................................................................................. 2 - 15 2.2 Soils and Geology…………………………………………………………………………….. 2 - 19 2.3 Sediment Quality …………………………………………………………………………….. 2 - 20 2.3.1 Evaluation of ISP Pond Sediments………………………………………….………….... 2 - 21 2.3.1.1 Alviso Complex................................................................................................................... 2 - 21 2.3.1.2 Baumberg Complex............................................................................................................. 2 - 26 2.3.1.3 West Bay Complex............................................................................................................... 2 - 28 2.4 Hydrology and Water Quality………………………………………………………………... 2 - 28 2.5 Hydraulic Setting……………………………………………………………………………...2 - 35 2.5.1 Physical Setting of South San Francisco Bay and Associated Tidal Sloughs ….. ………..2 - 35 2.5.1.1 South San Francisco Bay……………………………………………………………………..2 - 35 2.5.2 South San Francisco Bay Salinity………………………………………………………… 2 - 42 2.5.3 South San Francisco Bay Tidal Sloughs………………………………………………….. 2 - 47 2.5.3.1 Tidal Sloughs near the Alviso System.................................................................................2 - 47 2.5.3.2 Tidal Sloughs near the Baumberg System............................................................................... 2 - 50 2.5.3.3 Tidal Sloughs near the West Bay System................................................................................ 2 - 51 3.0 Development of the Management Plan 3.1 Goals and Objectives………………………………………………………………………….. 3 - 1 3.2 Opportunities, Constraints, and Costs………………………………………………………… 3 - 2 3.3 Salinity Simulations …………………………………………………………………………... 3 - 4 3.3.1 Pond Model …………………………………………………………………….………... 3 - 4 3.3.1.1 Hydraulic Information…………………………………………………………………….. 3 - 5 3.3.3 Simulation Period ………………………………………………………………………….3 - 6 iii Table of Contents 3.4 History of Project Design (Alternatives) ……………………………………………..……… 3 - 9 3.4.1 No Action…………………………………………………………………………………. 3 - 9 3.4.2 Maintain Infrastructure Only……………………………………………………………… 3 - 9 3.4.3 Culvert Structures for Island Ponds……………………………………...……………… 3 - 10 3.4.4 Seasonal Pond Operations…………………………………………………….………… 3 - 10 3.4.5 Flexibility in Time Period of Initial Release………………………………….………… 3 - 10 3.4.6 Individual System Alternative………………………………………………… ………...3 - 10 3.4.6.1 Alviso A3W System ………………………………………………………………………... 3 - 11 3.4.6.2 Alviso A7 System …………………………………………………………………………... 3 - 11 3.4.6.3 Alviso A14 System …………………………………………………………………………. 3 - 11 3.4.6.4 Alviso A16 System …………………………………………………………………………. 3 - 11 3.4.6.5 Baumberg 2 System ……………………………………………………………….………... 3 - 12 3.4.6.6 Baumberg 2C System ………………………………………………………………………. 3 - 12 3.4.6.7 Baumberg 8A System……………………………………………………………… ………. 3 - 12 3.4.6.8 Baumberg 6A System……………………………………………………………… ………. 3 - 12 4.0 Proposed Initial Stewardship Implementation Plan 4.1 General Project Description …………………………………………………………………... 4 - 1 4.1.1 Introduction and Summary……………………………………………………….………… 4 - 1 4.1.2 Overall Hydraulic Design ………………………………………………………………......4 - 1 4.1.3 Initial Salinity Releases ……………………………………………………………………..4 - 1 4.1.4 Pond Model Results ………………………………………………………………………...4 - 2 4.1.5 Maximum Initial Release Salinities ………………………………………………………...4 - 2 4.1.6 Long Term Discharge Salinities …………………………………………………………....4 - 4 4.1.7 Summary of Water Surface Elevations …………………………………………………......4 - 4 4.1.8 Water Control Structures …………………………………………………………………...4 - 8 4.1.9 Maintenance ………………………………………………………………………………..4 - 15 4.2. Detailed Description Pond Complex Operations………...………………………………….... 4 - 15 4.2.1 Alviso System A2W……………………………………………………………………..…4 - 15 4.2.1.1 Circulation Hydraulics ………………………………………………………………..….4 - 17 4.2.1.2 Interim Management Conditions …………………………………………………….…..4 - 17 4.2.1.3 Salinity …………………………………………………………………………………...4 - 18 4.2.1.4 Management Operations ………………………………………………………………...4 - 20 4.2.2 Alviso System A3W…………………………………………………………………….…. 4 - 20 4.2.2.1 Circulation Hydraulics ……………………………………………………………….…. 4 - 22 4.2.2.2 Interim Management Conditions …………………………………………………….…..4 - 22 4.2.2.3 Salinity …………………………………………………………………………………...4 - 23 4.2.2.4 Management Operations ………………………………………………………………....4 - 26 4.2.3 Alviso System A7………………………………………………………………………….. 4 - 26 4.2.3.1 Circulation Hydraulics ………………………………………………………………..….4 - 29 4.2.3.2 Interim Management Conditions…………………………………………………….…....4 - 29 4.2.3.3 Salinity …………………………………………………………………………………....4 - 30 4.2.3.4 Management Operations ……………………………………………………………….....4 - 33 4.2.4 Alviso System A14………………………………………………………………………..... 4 - 33 4.2.4.1 Circulation Hydraulics …………………………………………………………………...4 - 36 4.2.4.2 Interim Management Conditions ………………………………………………………....4 - 36 4.2.4.3 Salinity …………………………………………………………………………………....4 - 37 4.2.4.4 Management Operations ………………………………………………………………..…4 - 40 4.2.5 Alviso A16 System………………………………………………………………………..… 4 - 41 4.2.5.1 Circulation Hydraulics ………………………………………………………………..…..4 - 43 4.2.5.2 Interim Management Conditions ………………………………………………………....4 - 43 4.2.5.3 Salinity …………………………………………………………………………………....4 - 44 iv Table of Contents 4.2.5.4 Management Operations …………………………………………………………………4 - 46 4.2.6 Alviso Complex Island Ponds……………………………………………………………... 4 - 46 4.2.6.1 Circulation Hydraulics …………………………………………………………………..4 - 48 4.2.6.2 Interim Management Conditions ………………………………………………………..4 - 48 4.2.6.3 Salinity …………………………………………………………………………………...4 - 49 4.2.6.4 Management Operations …………………………………………………………………4 - 54 4.2.7 Alviso System A23………………………………………………………………………... 4 - 54 4.2.7.1 Circulation Hydraulics …………………………………………………………………..4 - 55 4.2.7.2 Interim Management Conditions ………………………………………………………..4 - 56 4.2.7.3 Management Operations ………………………………………………………………...4 - 56 4.2.8 Baumberg System 2……………………………………………………………………….. 4 - 56 4.2.8.1 Circulation Hydraulics …………………………………………………………………..4 - 58 4.2.8.2 Interim Management Conditions ………………………………………………………...4- 59 4.8.2.3 Salinity …………………………………………………………………………………..4 - 59 4.2.8.4 Management Operations ………………………………………………………………...4 - 62 4.2.9 Baumberg System 2C……………………………………………………………………… 4 - 62 4.2.9.1 Circulation Hydraulics …………………………………………………………………..4 - 64 4.2.9.2 Interim Management Conditions ………………………………………………………..4 - 65 4.2.9.3 Salinity …………………………………………………………………………………..4 - 67 4.2.9.4 Management Operations ………………………………………………………………...4 - 69 4.2.10 Baumberg System 6A……………………………………………………………………... 4 - 69 4.2.10.1 Circulation Hydraulics ……………………………………………………………………..4 - 71 4.2.10.2 Interim Management Conditions …………………………………………………………..4 - 72 4.2.10.3 Salinity ……………………………………………………………………………………..4 - 73 4.2.10.4 Management Operations …………………………………………………………………...4 - 76 4.2.11 Baumberg System 8A…………………………………………………………….………… 4 - 76 4.2.11.1 Circulation Hydraulics ……………………………………………………………………..4 - 78 4.2.11.2 Interim
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