Suisun Marsh Monitoring Program Annual Data Summary Water Year 1999

California Department of Water Resources (DWR) | July 31st, 2001

This report summarizes data collected in the Suisun Marsh during Water Year 1999 (October 1, 1998 through September 30, 1999) pursuant to the following agreements, perm

This report summarizes data collected in the Suisun Marsh during Water Year 1999 (October 1, 1998 through September 30, 1999) pursuant to the following agreements, permits, and water rights decisions: • State Water Resources Control Board Decision 1485, August 1978 (SWRCB 1978); • State Water Resources Control Board Order WR 95-6, 1995 (SWRCB 1995a); • Suisun Marsh Preservation Agreement, 1987 (USBR and others 1987); • Suisun Marsh Monitoring Agreement, 1987 (DWR and others 1987); • San Francisco Bay Conservation and Development Commission Permit No. 35-78 (M) Amendment 7, 1997 (for construction of the initial facilities, namely the Roaring River Distribution System, Morrow Island Distribution System, and Goodyear Slough Outfall) (BCDC 1997); • San Francisco Bay Conservation and Development Commission Permit No. 4-84 (M) Amendment 4, 1991 (for construction of the Suisun Marsh Salinity Control Gates) (1991); and, • U.S. Army Corps of Engineers Permit No. 16223E58 (for construction of the Suisun Marsh Salinity Control Gates), Special Condition 1, 1986 (USACE 1986). This report fulfills a portion of the annual reporting requirements of the above-listed, agreements, permits, and water rights decisions as detailed in Table 1. Remaining reporting requirements will be fulfilled in other Department of Water Resources (DWR) and/or University of California Davis reports. DWR and the California Department of Fish and Game (DFG) primarily collected data summarized in this report. The data include • general hydrologic data; • continuous channel water specific conductance and tidal height measurements; • marsh-wide vegetation survey update; • waterfowl abundance; and • salt marsh harvest mouse occurrence.

Summary of the MeHg Panels of the 2004 CalFed Science Conference

San Francisco Estuary Institute (SFEI) | November 22nd, 2004

Mercury (Hg) can become an environmental problem when sulfate-reducing anaerobic bacteria, in the presence of organic substrates, form methylmercury (MeHg), a highly toxi

Mercury (Hg) can become an environmental problem when sulfate-reducing anaerobic bacteria, in the presence of organic substrates, form methylmercury (MeHg), a highly toxic compound that endangers wildlife and people by accumulating in their food. The spatial and temporal variation in MeHg production is mainly a function of the availability of inorganic mercury to methylating bacteria. Typically only a small percentage (e.g. < 5 %) of total inorganic mercury is available for methylation. The amount of MeHg that actually becomes available for bioaccumulation depends on many environmental factors operating at different spatial scales, from watersheds to microbes. Scientists are working to prioritize these factors for management actions.

Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study

San Francisco Estuary Institute (SFEI) | February 1st, 2017

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and nat

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP). 

Syntheses of scientific knowledge for maintaining and improving functioning of the South Bay ecosystem and restoring tidal salt marsh and associated habitats

San Francisco Estuary Institute (SFEI) | October 1st, 2004

This synthesis focuses on the form and function of South Bay landscapes to address the following two issues – maintaining and improving functioning of the South Bay Eco

This synthesis focuses on the form and function of South Bay landscapes to address the following two issues – maintaining and improving functioning of the South Bay Ecosystem; and restoring tidal salt marsh and associated habitats over the next 50 years at pond and pond-complex levels. This synthesis is organized into five parts: (I) Definition of the South Bay Ecosystem; (II) Historical Conditions; (III) Landscape Modifications; (IV) Modern Conditions; and (V) Restoration Tools, Targets, and Related Questions. Specific topics posed by the Science Team Lead are addressed in each part of the synthesis.

The Delta as Changing Landscapes

University of California, Davis (UC Davis) | July 1st, 2016

What happens at one place in a landscape influences and is influenced by what happens in other places. Consequently, management and restoration that focus on individual p

What happens at one place in a landscape influences and is influenced by what happens in other places. Consequently, management and restoration that focus on individual places may fail to recognize and incorporate interactions across entire landscapes. The science of landscape ecology, which emphasizes the interplay of landscape structure, function, and change at multiple scales, offers a perspective that can integrate the spatial relationships of ecological processes and the functional interconnections of land and water in the Delta. Although the Delta is one of the most studied estuaries in the world, applications of landscape science have been limited. We describe why it is important to incorporate landscape science into management and restoration, emphasizing how Delta landscapes have changed over the past centuries. The land–water linkages of the past have been broken, waterways have been over-connected, and hard boundaries have replaced the gradual and dynamic transitions among landscape patches. The contemporary landscape also has new, novel assemblages of species and stressors that were not there in the past. This historical perspective indicates how knowledge of past landscape functions can contribute to the restoration and management of contemporary landscapes. We illustrate these points with case studies of inundation dynamics and riparian woodlands, and use a third example to describe a landscape approach to restoration. We propose that science that encompasses the multiple, interacting components of functional landscapes in the Delta will foster resilient and enduring restoration and management outcomes that benefit both people and wildlife. We suggest several ways of moving landscape science to the forefront of management and restoration in the Delta.

The effects of kaolin clay on the amphipod Eohaustorius estuarius: Part Two

San Francisco Estuary Institute (SFEI) | April 3rd, 2017

A number of lines-of-evidence suggest that the amphipod Eohaustorius estuarius has variable tolerance to clay in sediments. In Phase 1 of the current RMP special study, l

A number of lines-of-evidence suggest that the amphipod Eohaustorius estuarius has variable tolerance to clay in sediments. In Phase 1 of the current RMP special study, laboratory dose-response experiments were conducted in 2014 with kaolin clay to evaluate whether clay effects varied with amphipod size. The results indicated that smaller amphipods were more tolerant of clay than larger individuals. Average survival was 81%, 79%, and 65% for small, medium and large amphipods, respectively, in concentrations > 50% clay. As part of Phase 2 confirmation studies conducted in 2015-2016, the original kaolin dose-response experiments were repeated. Results of this experiment showed that average amphipod survival was 88%, 63%, and 41% for small, medium and large amphipods, respectively, in concentrations > 50% clay. Standard 96-hour reference toxicant tests with cadmium chloride (CdCl2) were conducted to determine whether there were size-specific differences in response to this metal reference toxicant. The CdCl2 median lethal concentrations (LC50s) for small, medium and large amphipods were 6.78, 5.13, and 4.63 mg/L, respectively. Responses of all three size classes to cadmium were within historic confidence intervals for this reference metal, and were not significantly different from one another based on overlapping confidence intervals. Additional experiments with high clay reference site sediments from San Francisco Bay were conducted to confirm the size related response with field sediments. The results confirm that use of smaller amphipods in routine monitoring of high clay sediments will reduce the influence of this factor on test results. 

Towards the Protection, Restoration, and Enhancement of the Delta Ecosystem: A Synthesis. Appendix A: Summary of Existing Habitat and Species-Specific Plans, Strategies, and Management Approaches

Delta Stewardship Council (Delta Council) | March 15th, 2018

USGS Science at Work in the Delta Estuary

U.S. Geological Survey (USGS) | November 19th, 2013

The San Francisco Bay and Sacramento-San Joaquin Delta form one of the largest estuaries in the United States. The “Bay-Delta” system provides water to more than 25 m

The San Francisco Bay and Sacramento-San Joaquin Delta form one of the largest estuaries in the United States. The “Bay-Delta” system provides water to more than 25 million California residents and vast farmlands, as well as key habitat for birds, fish, and other wildlife. To help ensure the health of this crucial estuary, the U.S. Geological Survey, in close cooperation with partner agencies and organizations, is providing science essential to addressing societal issues associated with water quantity and quality, sediment transportation, environmental contamination, animal health and status, habitat restoration, hazards, ground subsidence, and climate change.

Water Management Companion Plan (to the Statewide Wildlife Action Plan)

California Department of Fish and Wildlife (CDFW) | December 21st, 2016

The California State Wildlife Action Plan 2015 Update provides a vision and a framework for conserving California’s diverse natural heritage. SWAP 2015 also calls for t

The California State Wildlife Action Plan 2015 Update provides a vision and a framework for conserving California’s diverse natural heritage. SWAP 2015 also calls for the development of a collaborative framework to sustainably manage ecosystems across the state in balance with human uses of natural resources. To address the need for a collaborative framework, California Department of Fish and Wildlife (CDFW), Blue Earth Consultants, LLC (Blue Earth), and partner agencies and organizations undertook the preparation of companion plans for SWAP 2015. While this document reports on the progress made thus far on collaboration, the intent is to set a stage for achieving the state’s conservation priorities through continued partnerships and by mutually managing and conserving natural and cultural resources.

Yolo Bypass Salmonid Habitat Restoration and Fish Passage Implementation Plan

California Department of Water Resources (DWR) | September 21st, 2012

Significant modifications have been made to the historic floodplain of California‘s Central Valley for water supply and flood damage reduction purposes. The resulting l

Significant modifications have been made to the historic floodplain of California‘s Central Valley for water supply and flood damage reduction purposes. The resulting losses of rearing habitat, migration corridors, and food web production for fish have significantly hindered native fish species that rely on floodplain habitat during part or all of their life history. The Yolo Bypass (Bypass), which currently experiences at least some flooding in approximately 80% of years, still retains many characteristics of the historic floodplain habitat that are favorable to various fish species. In approximately 70% of years, Fremont Weir overtops, joining flows from western tributaries. In approximately 10% of years, localized flooding is due to western tributary contributions only (DWR 2008, Woodland gauge, unpublished analysis). The primary function of the Bypass is flood damage reduction, with most of it also managed as agricultural land. The Bypass has also been identified by several State and federal entities as a potential site for habitat restoration to ease pressure on and increase benefits to threatened and endangered fish species. On June 4, 2009, the National Marine Fisheries Service (NMFS) issued its Biological Opinion and Conference Opinion on the Long-term Operation of the Central Valley Project (CVP) and State Water Project (SWP) (NMFS Operation BO). The NMFS Operation BO concluded that, if left unchanged, CVP and SWP operations were likely to jeopardize the continued existence of four federally- listed anadromous fish species: Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, California Central Valley steelhead, and Southern Distinct Population Segment (DPS) North American green sturgeon. The NMFS Operation BO sets forth Reasonable and Prudent Alternative (RPA) actions that would allow continuing SWP and CVP operations to remain in compliance with the federal Endangered Species Act (ESA). This Yolo Bypass Salmonid Habitat Restoration and Fish Passage Draft Implementation Plan (Implementation Plan) was prepared jointly by the California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) to address two specific RPA Actions set forth in the NMFS Operation BO: RPA Action I.6.1: Restoration of Floodplain Rearing Habitat, through the increase of seasonal inundation within the lower Sacramento River basin; and RPA Action I.7: Reduce Migratory Delays and Loss of Salmon, Steelhead, and Sturgeon, through the modification of Fremont Weir and other structures of the Yolo Bypass. As mandated by the NMFS Operation BO, this Implementation Plan describes the activities, process, and timeline required to implement actions to address the requirements of RPA Actions I.6.1 and I.7. Major California restoration planning efforts over several decades (e.g., CALFED, the Bay Delta Conservation Plan) have focused on the Yolo Bypass as a prime area of the Sacramento Valley for enhancement of seasonal floodplain rearing habitat. The Yolo Bypass is generally seen as one of the best places in the lower Sacramento River Basin on which to focus implementation resources in order to achieve implementation of floodplain enhancements because of these efforts. Some of the technical foundation for these efforts has been well laid and interaction with stakeholders and local property owners has been initiated and is on-going. Implementation procedures related to RPA Action I.6.1 within the NMFS Operation BO specify that this Implementation Plan include an evaluation of options to "increase aquatic inundation of publicly and privately owned suitable acreage within the Yolo Bypass." Therefore, this Implementation Plan focuses on restoration of floodplain rearing habitat within the Yolo Bypass to address RPA Action I.6.1. However, the planning and environmental compliance process will consider a reasonable range of alternatives for implementing this RPA action. Additional discussion regarding the availability and suitability of areas for seasonal floodplain inundation is provided in Section 6: Proposals to Refine the RPA Actions.