Three-Dimensional Modeling of Hydrodynamics and Salinity in the San Francisco Estuary: An Evaluation of Model Accuracy, X2, and the Low-Salinity Zone

Abstract

The three-dimensional UnTRIM San Francisco Bay-Delta model was applied to simulate tidal hydrodynamics and salinity in the San Francisco Estuary (estuary) using an unstructured grid. We compared model predictions to observations of water level, tidal flow, current speed, and salinity collected at 137 locations throughout the estuary. A quantitative approach based on multiple model assessment metrics was used to evaluate the model's accuracy for each comparison. These comparisons demonstrate that the model accurately predicted water level, tidal flow, and salinity during a 3-year simulation period that spanned a large range of flow and salinity conditions. The model is therefore suitable for detailed investigation of circulation patterns and salinity distributions in the estuary. The model was used to investigate the location, and spatial and temporal extent of the low-salinity zone (LSZ), defined by salinity between 0.5 and 6 psu. We calculated X2, the distance up the axis of the estuary to the daily-averaged 2-psu near-bed salinity, and the spatial extent of the LSZ for each day during the 3-year simulation. The location, area, volume, and average depth of the low-salinity zone varied with X2; however this variation was not monotonic and was largely controlled by the geometry of the estuary. We used predicted daily X2 values and the corresponding daily Delta outflow for each day during the 3-year simulation to develop a new equation to relate X2 to Delta outflow. This equation provides a conceptual improvement over previous equations by allowing the time constant for daily changes in X2 to vary with flow conditions. This improvement resulted in a smaller average error in X2 prediction than previous equations. These analyses demonstrate that a well-calibrated three-dimensional (3-D) hydrodynamic model is a valuable tool for investigating the salinity distributions in the estuary, and their influence on the distribution and abundance of physical habitat.

Linking Hydrodynamic Complexity to Delta Smelt (Hypomesus transpacificus) Distribution in the San Francisco Estuary, USA

“…The UnTRIM hydrodynamic model has been implemented in the San Francisco Bay and Sacramento-San Joaquin Delta to simulate tides, inflows and water diversions, water surface elevations, 3-D velocities, and salinity throughout the Bay-Delta system (MacWilliams et al 2015). The UnTRIM Bay-Delta model spans the entire estuary, from the Pacific Ocean through the Sacramento River and San Joaquin River (Figure 2).…”

“…We used a two-equation turbulence closure model, choosing parameter values of the generic length-scale equation from Warner et al (2005) to yield the k-ε closure (Umlauf and Burchard 2003). MacWilliams et al (2015) presented a detailed description of the model boundary conditions and forcing. The UnTRIM Bay-Delta Model has been used previously to examine the location of the 2 psu isohaline in San Francisco Bay (MacWilliams et al 2015), for studies of fish habitat (Kimmerer et al …”

“…MacWilliams et al (2015) presented a detailed description of the model boundary conditions and forcing. The UnTRIM Bay-Delta Model has been used previously to examine the location of the 2 psu isohaline in San Francisco Bay (MacWilliams et al 2015), for studies of fish habitat (Kimmerer et al …”

“…We focused on the easternmost embayment, Suisun Bay, comprising two relatively flat and shallow sub-embayments: Grizzly Bay and Honker Bay (Figure 1). During fall, the Low Salinity Zone (LSZ), the portion of the estuary with salinity between 0.5 and 6 psu, is often in the vicinity of Suisun Bay (MacWilliams et al 2015). Although there is a net westward water flow through Suisun Bay resulting from the freshwater outflow from the Delta, the currents within Suisun Bay are primarily driven by the interaction of the semidiurnal tides with a complicated bathymetry (Cheng and Gartner 1984).…”

Long-Term Surveys Show Invasive Overbite Clams (Potamocorbula amurensis) are Spatially Limited in Suisun Marsh, California

“…Because salinity is such a strong driver of abundance and distribution of overbite clams, the effect of different freshwater sources on Suisun Marsh -such as Delta outflow (MacWilliams et al 2015), ephemeral creeks (O'Rear and Moyle 2013), wastewater-treatment discharges (Siegel 2014), and in-marsh water diversions (Laćan and Resh 2016) -should be assessed to elucidate more finescale effects of freshwater inflows. Given overbite clam's high filtration rates (Greene et al 2011), their high abundance in lower Suisun Slough could reduce the supply of phytoplankton and zooplankton transported up the slough from Grizzly Bay to smaller, more interior sloughs.…”