San Francisco Estuary and Watershed Science

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.

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.