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Research about San Francisco Bay-Delta Estuary

Source-linked reports with geographic coverage including San Francisco Bay-Delta Estuary.

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Bivalves

Bivalves are important as consumers of pelagic and demersal food resources. With sufficient biomass, they can compete with and, in some cases, outcompete other members of the pelagic food web for food resources such as phytoplankton and zooplankton. We include bivalves in the San Francisco Estuary (SFE) and Delta in the FLOAT MAST because they have been and continue to be an important member of the food web. Changes in the bivalves over the last 40 years have led us to hypothesize that bivalves may limit food resources for Delta Smelt and other pelagic fish species (Kimmerer and Thompson 2014, Sommer et al 2007). We will discuss the two bivalves with the largest biomass, the estuarine bivalve Potamocorbula amurensis (hereafter Potamocorbula ) and the freshwater bivalve Corbicula fluminea (hereafter Corbicula ). The distribution of these two species together covers the full range of salinities between the Golden Gate and the upstream reaches of the SR and SJR. The species overlap in the region of X2. Both species’ distributions expand or contract when the salinity distribution changes and do so in near synchrony with each other at a salinity of approximately 2. It is this interaction of both bivalves at their threshold levels of salinity within the ecologically sensitive low salinity zone (LSZ) in addition to their distribution in the rest of the system that determines each species effect on the food web.

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A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California

Climate change, sea-level rise, and human development have contributed to the changing geomorphology of the San Francisco Bay - Delta (Bay-Delta) Estuary system. The need to predict scenarios of change led to the development of a new seamless, high-resolution digital elevation model (DEM) of the Bay – Delta that can be used by modelers attempting to understand potential future changes to the estuary system. This report details the three phases of the creation of this DEM. The first phase took a bathymetric-only DEM created in 2005 by the U.S. Geological Survey (USGS), refined it with additional data, and identified areas that would benefit from new surveys. The second phase began a USGS collaboration with the California Department of Water Resources (DWR) that updated a 2012 DWR seamless bathymetric/topographic DEM of the Bay-Delta with input from the USGS and modifications to fit the specific needs of USGS modelers. The third phase took the work from phase 2 and expanded the coverage area in the north to include the Yolo Bypass up to the Fremont Weir, the Sacramento River up to Knights Landing, and the American River up to the Nimbus Dam, and added back in the elevations for interior islands. The constant evolution of the Bay-Delta will require continuous updates to the DEM of the Delta, and there still are areas with older data that would benefit from modern surveys. As a result, DWR plans to continue updating the DEM.

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Conceptual model for invasive bivalve control on wetland productivity

Tidal wetlands were the historically dominant features of many coastal regions around the world, including the San Francisco Estuary (Callaway et al. 2011; Whipple et al. 2012). These mosaics of varied interconnected habitats (Mitsch and Gosselink 1993) provide a host of ecosystem services, including biodiversity maintenance, fish and wildlife habitat, water quality improvement, flood abatement, and carbon sequestration (Rabenhorst 1995; Costanza et al. 1997; Bottom et al. 2005; Zedler and Kercher 2005; Barbier et al. 2010). They also support human activities and values such as recreation and aesthetic appreciation (Barbier et al. 2010; Milligan and Kraus-Polk 2016). Despite their critical functions, many wetland landscapes have been destroyed or irreparably altered, either incidentally or intentionally, by human activities (Holland et al. 2004; Zedler and Kercher 2005; Callaway et al. 2011; Cloern and Jassby 2012; Whipple et al. 2012; Schile et al. 2014). San Francisco Estuary (SFE) (see Figure 1) tidal wetlands were largely converted to other land uses in the late 1800s and early 1900s, with the extent of loss and new use varying by region. Wetland losses in the North, Central, and South San Francisco bays and Suisun Bay ranged from 70 percent to 93 percent to accommodate agricultural uses, salt production, managed waterfowl habitat, and urban development (Callaway et al. 2011). Landscape transformation within the most inland portion of the SFE, the Sacramento-San Joaquin Delta (Delta), was even more dramatic. Overall, today’s Delta contains 97 percent less freshwater tidal wetland than its historical state and nearly double the open water area (Whipple et al. 2012). The majority of the modern Delta consists of agricultural tracts protected from tidal waters by human-made dikes or levees, which are commonly armored with riprap. The de-watered, rich peat soils of these created islands have supported abundant agricultural production, but have oxidized, compacted, and blown away in the process, causing significant subsidence (Deverel and Leighton 2010). Occasional levee failures turn islands into lakes; a few large shallow lakes remain after accidental levee breaches were not repaired (Whipple et al. 2012).

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High-resolution remote sensing of water quality in the San Francisco Bay-Delta Estuary

The San Francisco Bay–Delta Estuary watershed is a major source of freshwater for California and a profoundly human-impacted environment. The water quality monitoring that is critical to the management of this important water resource and ecosystem relies primarily on a system of fixed water-quality monitoring stations, but the limited spatial coverage often hinders understanding. Here, we show how the latest technology in visible/near-infrared imaging spectroscopy can facilitate water quality monitoring in this highly dynamic and heterogeneous system by enabling simultaneous depictions of several water quality indicators at very high spatial resolution. The airborne portable remote imaging spectrometer (PRISM) was used to derive high-spatial-resolution (2.6 × 2.6 m) distributions of turbidity, and dissolved organic carbon (DOC) and chlorophyll-a concentrations in a wetland-influenced region of this estuary. A filter-passing methylmercury vs DOC relationship was also developed using in situ samples and enabled the high-spatial-resolution depiction of surface methylmercury concentrations in this area. The results illustrate how high-resolution imaging spectroscopy can inform management and policy development in important inland and estuarine water bodies by facilitating the detection of point- and nonpoint-source pollution, and by providing data to help assess the complex impacts of wetland restoration and climate change on water quality and ecosystem productivity.

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Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological effects of a proposed San Luis drain extension

During the next few years, federal and state agencies may be required to evaluate proposals and discharge permits that could significantly change selenium (Se) inputs to the San Francisco Bay-Delta Estuary (Bay-Delta), particularly in the North Bay (i.e., Suisun Bay and San Pablo Bay). These decisions may include discharge requirements for an extension of the San Luis Drain (SLD) to the estuary to convey subsurface agricultural drainage from the western San Joaquin Valley (SJV), a renewal of an agreement to allow the existing portion of the SLD to convey subsurface agricultural drainage to a tributary of the San Joaquin River (SJR) (coincident with changes in flow patterns of the lower SJR), and refinements to promulgated Se criteria for the protection of aquatic life for the estuary. Understanding the biotransfer of Se is essential to evaluating the fate and impact of proposed changes in Se discharges to the Bay-Delta. However, past monitoring programs have not addressed the specific protocols necessary for an element that bioaccumulates. Confusion about Se threats in the past have stemmed from failure to consider the full complexity of the processes that result in Se toxicity. Past studies show that predators are more at risk from Se contamination than their prey, making it difficult to use traditional methods to predict risk from environmental concentrations alone. In this report, we employ a novel procedure to model the fate of Se under different, potentially realistic load scenarios from the SJV. For each potential load, we progressively forecast the resulting environmental concentrations, speciation, transformation to particulate form, bioaccumulation by invertebrates, trophic transfer to predators, and effects in those predators. Enough is known to establish a first order understanding of effects should Se be discharged directly into the North Bay via a conveyance such as the SLD. Our approach uses 1) existing knowledge concerning the biogeochemical reactions of Se (e.g., speciation, partitioning between dissolved and particulate forms, and bivalve assimilation efficiency) and 2) site-specific data mainly from 1986 to 1996 on clams and bottom-feeding fish and birds. Forecasts of Se loading from oil refineries and agricultural drainage from the SJV enable the calculation of a composite freshwater endmember Se concentration at the head of the estuary and at Carquinez Strait as a foundation for modeling. Our analysis of effects also takes into account the mode of conveyance for agricultural drainage (i.e., the SLD or SJR). The effects of variable flows on a seasonal or monthly basis from the Sacramento River and SJR are also considered. The results of our forecasts for external SJV watershed sources of Se mirror predictions made since 1955 of a worsening salt (and by inference, Se) buildup exacerbated by the arid climate and irrigation for agricultural use. We show that the reservoir of Se in the SJV is sufficient to provide loading at an annual rate of approximately 42,500 pounds (lbs) of Se to a Bay-Delta disposal point for 63 to 304 years at the lower range of our projections, even if influx of Se from the California Coast Ranges could be curtailed. Disposal of wastewaters on an annual basis outside of the SJV may slow the degradation of valley resources, but drainage alone cannot alleviate the salt and Se buildup in the SJV, at least within a century. Our forecasts show the different proportions of Se loading to the Bay-Delta. Oil refinery loads from 1986 to 1992 ranged from 11 to 15 lbs Se per day; with treatment and cleanup, loads decreased to 3 lbs Se per day in 1999. In contrast, SJV agricultural drainage loads could range from of 45 to 117 lbs Se per day across a set of reasonable conditions. Components of this valley-wide load include five source subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) based on water and drainage management. Loads vary per subarea mainly because of proximity of the s

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