San Francisco Estuary and Watershed Science

Circulation in Clifton Court Forebay (CCF) was simulated using the three-dimensional (3–D) hydrodynamic model UnTRIM. These numerical simulations were performed to provide a better understanding of circulation patterns, flow pathways, and residence time in Clifton Court Forebay in support of ongoing studies of pre-screen loss and fish facility efficiency for delta smelt (Hypomesus transpacificus) at the California State Water Project (SWP) export facilities. The 3–D hydrodynamic model of CCF was validated through comparisons to observed water surface elevations inside CCF, and comparisons to observed drifter paths and velocity measurements collected by the U.S. Geological Survey as part of this study. Flow measurements collected near the radial gates for 2 days during relatively low inflows suggest that the Hills (1988) gate equations may over-estimate inflow by as much as 39% when the CCF radial gates are only partially opened. Several alternative approaches to improve the implementation of the radial gate flows in the UnTRIM model were evaluated. The resulting model accurately predicts water surface elevations and currents inside CCF over a range of wind and operating conditions. The validated model was used to predict residence time and other transport time scales for two 21-day simulation periods, one of very low daily SWP export pumping averaging 19.3 m³ s^-1 and one for moderate daily SWP export pumping averaging 66.6 m³ s^-1. The average transit time, indicating the time from entering CCF to reaching the fish facility, was estimated as 9.1 days for low export conditions and 4.3 days for moderate export conditions.  These transport time scale estimates may be used to inform estimates of pre-screen losses inside CCF due to predation or other causes.

A primary goal of the Central Valley Project Improvement Act is to at least double natural production of Chinook salmon (Oncorhynchus tshawytscha), in California Central Valley (CV) streams on a sustainable basis. Achievement relies on restoration actions that involve both discharge (e.g., dam releases) and non-discharge (e.g., gravel augmentation, screening) components. Annual adult and juvenile abundance estimates for individual watersheds must be tracked to assess effectiveness of individual actions. However, to date, no substantial efforts have been taken to demonstrate success or deficiencies of their implementations. A major challenge in interpreting time series of counts at any one life stage is that they reflect the cumulative effects of both freshwater and marine factors over the full life cycle. To address this issue, we developed a conceptual framework based on ratios of the abundance of consecutive CV fall-run Chinook salmon life stages and how variation in these ratios tracks key independent variables during the freshwater portion of the life cycle. Model validation with several case studies shows that estimates of previous stage class production correlate well with estimated individuals produced in the next class, indicating that transition rates tend to vary within a constrained range, and that monitoring programs generate abundance estimates whose errors are small enough not to swamp out the underlying signal. When selected environmental parameters were added to demonstration models, abundance estimates were more closely modeled and several tested relationships between environmental drivers and life-stage transition rates proved consistent across watersheds where data were available. Results from this generalized life-stage conceptual model suggest a potential framework for tracking the success of actions meant to improve survival for a given life stage within an individual stream and for determining how successive stages respond to these changes. Though examples are provided for CV Chinook salmon, these concepts can be applied wherever migratory salmonid populations and associated environmental data are being adequately monitored.

Erratum dated 2014 June 25

Pharmaceuticals and personal care products (PPCPs) are found in surface waters worldwide. Wastewater treatment plant effluent is a major source of these contaminants. The Sacramento–San Joaquin Delta (Delta) is a unique aquatic ecosystem, a source of drinking water for over 25 million Californians, and a primary source of water for Central Valley agriculture. The sharp decline of four pelagic fish species in the Delta in the last decade is just one of several indicators that the ecosystem is severely impaired. Several wastewater treatment plants (WWTPs) discharge into the Delta, directly or through tributaries. The presence of PPCPs in the Delta has received very little attention relative to the immense effort underway to rehabilitate the ecosystem. This study determined concentrations of PPCPs in the Sacramento River in the vicinity of the Sacramento Regional Wastewater Treatment Plant using passive sampler monitoring. These data were used to estimate loads of three of the detected pharmaceuticals (carbamazepine, fluoxetine, and trimethoprim) from nine other WWTPs that discharge to the Delta. The 2-D, finite element, Resource Management Associates (RMA) Delta Model was then applied to determine the distribution that might result from these discharges. The model was run for the 2006, 2007, and 2009 water years. Results indicate that it is feasible that WWTP discharges could result in chronic presence of these pharmaceuticals at low ng L^-1 levels at all 45 model output locations and, therefore, aquatic organisms within the Delta may be continually exposed to these contaminants.

We used a combination of published literature and field survey data to synthesize the available information about habitat use by delta smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Delta smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin rivers. In recent years, substantial numbers of delta smelt have colonized habitat in Liberty Island, a north Delta area that flooded in 1997. The species has a more upstream distribution during spawning as opposed to juvenile rearing periods. Post-larvae and juveniles tend to have a more downstream distribution during wetter years. Delta smelt are most common in low-salinity habitat (<6 psu) with high turbidities (>12 NTU) and moderate temperatures (7 °C to 25 °C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water-residence times (e.g. tidal marsh, shoal, low-order channels) may be favorable. Other desirable features of delta smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation (SAV) and the toxic algae Microcystis. Although enough is known to plan for large-scale pilot habitat projects, these efforts are vulnerable to several factors, most notably climate change, which will change salinity regimes and increase the occurrence of lethal temperatures. We recommend restoration of multiple geographical regions and habitats coupled with extensive monitoring and adaptive management. An overall emphasis on ecosystem processes rather than specific habitat features is also likely to be most effective for recovery of the species.