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Suisun Marsh Salinity Gates Pilot Study Project Description

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Suisun Marsh Salinity Gates Pilot Study Project Description Prepared for: California Department of Water Resources March 2018 Prepared by: Consulting Engineers and Scientists Suisun Marsh Salinity Gates Pilot Study Project Description Prepared for: California Department of Water Resources 3500 Industrial Boulevard, 2nd Floor West Sacramento, CA 95691 Contact: Michal Koller (916) 376-9728 Prepared by: GEI Consultants, Inc. 2868 Prospect Park Drive, Suite 400 Sacramento, CA 95670 Contact: Nicholas Tomera Project Manager (916) 912-4942 March 20, 2018 Project No. 1701316 1.1 Table of Contents Abbreviations and Acronyms .................................................................................................................................. ii Chapter 1. Introduction ..................................................................................................................................... 1 1.1 Background ......................................................................................................................... 1 1.1.1 Delta Smelt Resiliency Strategy ............................................................................. 1 1.1.2 Permits ................................................................................................................... 1 1.2 Pilot Study Summary ........................................................................................................... 1 Chapter 2. Suisun Marsh Salinity Control Gates Operation ......................................................................... 2 Chapter 3. Modelling Results ........................................................................................................................... 4 Chapter 4. 2018–2020 Pilot Study ................................................................................................................... 5 4.1 Operations ........................................................................................................................... 5 4.2 Monitoring and Assessment ................................................................................................ 6 Chapter 5. Summary of Anticipated Effects ................................................................................................... 7 5.1 Water Quality ....................................................................................................................... 7 5.2 Fish ...................................................................................................................................... 7 5.3 Wetlands .............................................................................................................................. 7 5.4 Recreation ........................................................................................................................... 7 Chapter 6. References ...................................................................................................................................... 8 Tables Table 1. Typical Gates Operations ................................................................................................................. 3 Figures Figure 1. Suisun Marsh Vicinity Map ............................................................................................................... 2 Figure 2. Proposed 2018 Operational Schedule for the Pilot Study ................................................................ 5 Department of Water Resources GEI Consultants, Inc. Proposed Action #4 i Abbreviations and AcronymsTable of Contents Abbreviations and Acronyms ADP adaptive management planning BO Biological Opinion DBW Division of Boating and Waterways DWR Department of Water Resources EC electric conductivity fps feet per second Gates Suisun Marsh Salinity Control Gates IEP Interagency Ecology Program NMFS National Marine Fisheries Service USCG U.S. Coast Guard USFWS US Fish and Wildlife Service GEI Consultants, Inc. Department of Water Resources Abbreviations and Acronyms ii Proposed Action #4 Chapter 1. Introduction 1.1 Background 1.1.1 Delta Smelt Resiliency Strategy California Department of Water Resources (DWR) is evaluating the feasibility of implementing Action #4 in the Delta Smelt Resiliency Strategy (Resources Agency, 2016) which calls for summer operation of the Suisun Marsh Salinity Control Gates as described below: Linkage to Conceptual Models This management action is proposed as an alternative to the Summer Outflow Augmentation action described above and would benefit juvenile and sub-adult life Delta Smelt stages. The primary Habitat Attribute that would be affected is Food Availability. Summary of Action DWR will operate the Suisun Marsh Salinity Control Gates to reduce salinity in the Suisun Marsh during summer months. This management action may attract Delta Smelt into the high-quality Suisun Marsh habitat and reduce their use of the less food-rich Suisun Bay habitat. This management action would need to be monitored closely to ensure it does not result in unintended salinity changes in Suisun Bay, the Sacramento/San Joaquin River confluence region, or key water quality compliance/export locations. 1.1.2 Permits Operation of the Suisun Marsh Salinity Control Gates (Gates) was evaluated in the 2009 National Marine Fisheries Service (NMFS) Biological Opinion (BO) (2008/09022) and 2008 U.S. Fish and Wildlife Service (USFWS) BO (81420-2008-F-1481-5) for the Long-Term Operations of the Central Valley Project and State Water Project. Telemetry studies conducted from 1998 through 2004 identified a significant improvement in salmonid passage when the boat locks were left open. As a result, the MNFS BO mandate that the boat locks remain in the open position while the flashboards are in place. DWR currently holds a permit for operation and maintenance for Gates with the San Francisco Bay Conservation and Development Commission (Permit 1984.004.007md) which is valid through April 1, 2020. DWR will apply for a minor amendment to authorize this work under the current permit. 1.2 Pilot Study Summary DWR proposes to undertake a Pilot Study which involves operating the Gates in August 2018, 2019, and 2020, depending on suitable conditions within the Suisun Marsh as determined by DWR modeling. Overall, the effort represents a modest change to normal operations of the Suisun Marsh Salinity Control Gates. DWR will monitor the Pilot Study operations to determine if it is effective at enhancing Delta smelt habitat in select locations throughout the Suisun Marsh. The results of the Pilot Study will help inform both the efficacy of summer Gates operations on improving Delta Smelt habitat and will also support development and permitting of a more permanent operations plan, as needed. Department of Water Resources GEI Consultants, Inc. Proposed Action #4 1 Introduction Chapter 2. Suisun Marsh Salinity Control Gates Operation The Gates, which aid in reducing salinity throughout the Suisun Marsh, are in the eastern portion of Montezuma Slough approximately 3 miles north of Collinsville (Figure 1). The Gates are one of the four initial facilities (outlined in the Suisun Marsh Preservation Agreement of 1987) and began operating in November 1988. Figure 1. Suisun Marsh Vicinity Map Source: ICF The Gates are a structure that consist of radial gates, flashboards, and a boat lock. Currently, the Gates begin tidally-operating in early October, depending on salinity, and may continue through the end of May. This period is referred to as the control season. During the control season, the radial gates are lowered during the flood tides and opened during the ebb tides (i.e., tidally operated), flashboards are installed, and the boat lock is operated as-needed for passing vessels. Outside of the control season, the radial gates remain open (allowing unrestricted tidal flow), the flashboards are removed, and the operation of the boat lock is not needed. Table 1 summarizes the typical operations of the Gates. GEI Consultants, Inc. Department of Water Resources Suisun Marsh Salinity Control Gates Operation 2 Proposed Action #4 Table 1. Typical Gates Operations Period Radial Gates Flashboards Boat Lock Control Season October – May Tidally-operated* Installed Operated Non-Control Season June – September Open Removed Not Operated Note: * Depends on salinity. Understanding how the Gates work requires an understanding of the hydrology of Montezuma Slough without the Gates. Montezuma Slough runs in a semicircular route from the Sacramento River–San Joaquin River confluence downstream to Grizzly Bay. During flood tide, flow typically goes from west to east depending upon the magnitude of Delta outflow, where the flow from Grizzly Bay is dominant. By convention, this flow direction is considered to be negative. At high tide, a slack water condition typically occurs, and the flow slows to zero. Then, as ebb tide begins, flow goes from east to west, where the flow from the Delta is dominant. This flow direction is considered positive. At low tide, a slack water conditions once again occurs, with the flow slowing to zero. The process then repeats. The Gates control salinity by allowing tidal flow from the Sacramento River into Montezuma Slough during ebb (outgoing) tides but restricting the tidal flow from Montezuma Slough during flood (incoming) tides. The Gates cause a net inflow (approximately 2,500 cubic feet per second) of low salinity Sacramento River water into Montezuma Slough. When sensors detect a velocity of -+0.1 feet per second (fps) the Gates automatically
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