SFEWS Vol. 20, Issue 2 | June 2022
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review
Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems, particularly in estuaries. In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Volume 8, Issue 3, 2010
High variability in environmental conditions in both space and time once made the upper San Francisco Estuary (the Estuary) highly productive for native biota. Present conditions often discourage native species, providing a rationale for restoring estuarine variability and habitat complexity. Achieving a variable, more complex Estuary requires policies which: (1) establish internal Sacramento–San Joaquin Delta (the Delta) flows that create a tidally mixed, upstream–downstream gradient in water quality, with minimal cross-Delta flows; (2) create slough networks with more natural channel geometry and less diked, riprapped channel habitat; (3) increase inflows from the Sacramento and San Joaquin rivers; (4) increase tidal marsh habitat, including shallow (1 to 2 m) subtidal areas, in both fresh and brackish zones of the Estuary; (5) create/allow large expanses of low salinity (1 to 4 ppt) open water habitat in the Delta; (6) create a hydrodynamic regime where salinities in the upper Estuary range from near-fresh to 8 to 10 ppt periodically, to discourage alien species and favor desirable species; (7) take species-specific actions that reduce abundance of non-native species and increase abundance of desirable species; (8) establish abundant annual floodplain habitat, with additional large areas that flood in less frequent wet years; (9) reduce inflow of agricultural and urban pollutants; and (10) improve the temperature regime in large areas of the Estuary so temperatures rarely exceed 20 °C during summer and fall months. These actions collectively provide a realistic if experimental approach to achieving flow and habitat objectives to benefit desirable species. Some of these goals are likely to be achieved without deliberate action as the result of sea level rise, climate change, and levee failures, but in the near term, habitat, flow restoration and export reduction projects can enhance a return to a more variable and more productive ecosystem.
Two multibeam sonar surveys of west-central San Francisco Bay, California, were conducted in 1997 and 2008. Bathymetric change analysis between the two surveys indicates a loss of 14.1 million cubic meters (-3.1 cm/yr) of sediment during this time period, representing an approximately three-fold acceleration of the rate that was observed from prior depth change analysis from 1947 to 1979 for all of Central Bay, using more spatially coarse National Ocean Service (NOS) soundings. The portions of the overlapping survey areas between 1997 and 2008 designated as aggregate mining lease sites lost sediment at five times the rate of the remainder of west-central San Francisco Bay. Despite covering only 28% of the analysis area, volume change within leasing areas accounted for 9.2 million cubic meters of sediment loss, while the rest of the area lost 4.9 million cubic meters of sediment. The uncertainty of this recent analysis is more tightly constrained due to more stringent controls on vertical and horizontal position via tightly coupled, inertially aided differential Global Positioning Systems (GPS) solutions for survey vessel trajectory that virtually eliminate inaccuracies from traditional tide modeling and vessel motion artifacts. Further, quantification of systematic depth measurement error can now be calculated through comparison of static surfaces (e.g., bedrock) between surveys using seafloor habitat maps based on acoustic backscatter measurements and ground-truthing with grab samples and underwater video. Sediment loss in the entire San Francisco Bay Coastal System during the last half-century, as estimated from a series of bathymetric change studies, is 240 million cubic meters, and most of this is believed to be coarse sediment (i.e., sand and gravel) from Central Bay and the San Francisco Bar, which is likely to limit the sand supply to adjacent, open-coast beaches. This hypothesis is supported by a calibrated numerical model in a related study that indicates that there is a potential net export of sand-sized sediment across the Golden Gate, suggesting that a reduction in the supply of sand-sized sediment within west-central San Francisco Bay will limit transport to the outer coast.
Land use is an ultimate driver of many of the stressors on the Upper San Francisco Estuary, but the magnitude and pattern of land use change has not been analyzed. This paper attempts to fill this knowledge gap through a screening-level risk assessment. Urban land use was compared within hydrodynamic subregions in 1990, 2000, and 2006. Ancillary data were then used to quantify secondary measures such as impervious cover, housing density, road density and road crossings. Despite the rapid growth of the Bay Area, Sacramento, and Stockton metropolitan areas, the percentage of urban area and rates of change in the subregions are generally low to moderate when compared to other estuaries in the United States. The spatial data sets used in this analysis have been posted online to a public repository to be used by other researchers.
Current and Long-Term Effects of Delta Water Quality on Drinking Water Treatment Costs from Disinfection Byproduct Formation
Sea level rise and the failure of subsided western islands are likely future conditions for the Sacramento-San Joaquin Delta. This study explores the current and long-term effects of changes in the Delta’s water quality on drinking treatment costs for alternative disinfection and additional disinfection byproduct (DBP) precursor removal. Current and likely future Delta water qualities were investigated for electrical conductivity and the concentrations of bromide, and organic carbon. With roughly 1.5 million acre-feet (af) per year of Delta water used for urban water supplies, the drinking water treatment cost differences of taking water from the south Delta and the Sacramento River upstream could amount to $30 to $90 million per year currently, and could rise to $200 to $1000 million per year in the future, with lower water quality and urban use of Delta waters rising to 2 million af annually. From these results, waters drawn directly from the Delta will likely become more difficult and expensive to treat, making the Delta less desirable as a conventional water source.