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Kimmerer W.J.,San Francisco State University | MacWilliams M.L.,Delta Modeling Associates Inc. | Gross E.S.,Resources Management Associates Inc.
San Francisco Estuary and Watershed Science | Year: 2013

We used the UnTRIM San Francisco Bay-Delta hydrodynamic model to examine the spatial distribution of salinity as a function of freshwater flow in the San Francisco Estuary. Our particular focus was the covariation of flow with the spatial extent of the low-salinity zone (LSZ: salinity = 0.5 to 6), and with the extent of habitat for common species of nekton as defined by their salinity ranges. The UnTRIM model has an unstructured grid which allowed us to refine earlier estimates of the availability of suitable salinity ranges, particularly for species resident in low salinity. The response of the salinity field to flow was influenced by the bathymetry of the estuary. Area and volume of the LSZ were bimodal with X2, the distance up the axis of the estuary to a nearbottom salinity of 2, roughly the middle of the LSZ. The smallest area and volume occurred when the LSZ was in the Delta or Carquinez Strait, moderate values when it was in Suisun Bay, and the highest values when it was in broad, shallow San Pablo Bay. Resource selection functions for the distributions of common nekton species in salinity space were updated from previous values and used to calculate salinity-based habitat indices using the UnTRIM results. These indices generally increased with decreasing X2 (increasing flow), but the slopes of these relationships were mostly inconsistent with corresponding relationships of abundance to flow. Thus, although the salinity range used by most nekton expands as flow increases, other mechanisms relating population size to flow are likely more important than the physical extent of suitable salinity. © 2013 by the article author(s). Source


MacWilliams M.L.,Delta Modeling Associates Inc. | Gross E.S.,Resource Management Associates Inc.
San Francisco Estuary and Watershed Science | Year: 2013

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 comparisonsto 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 toimprove 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. Source


MacWilliams M.L.,Delta Modeling Associates Inc. | Bever A.J.,Delta Modeling Associates Inc. | Gross E.S.,Resource Management Associates Inc. | Ketefian G.S.,Resource Management Associates Inc. | And 3 more authors.
San Francisco Estuary and Watershed Science | Year: 2015

The three-dimensional UnTRIM San Francisco Bay- Delta model was applied to simulate tidal hydrodynamics and salinity in the San Francisco Estuary using an unstructured grid. Model predictions were compared 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 accuracy for each comparison. These comparisons demonstrate that the model accurately predicted water level, tidal flow, and salinity during a three year simulation period which 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. X2, the distance up the axis of the estuary to the daily-averaged 2 psu near-bed salinity, and the spatial extent of the low-salinity zone were calculated for each day during the three-year simulation. The location, area, volume, and average depth of the lowsalinity zone varied with X2; however this variation was not monotonic and was largely controlled by bathymetric features. Predicted daily X2 values and the corresponding daily Delta outflow for each day during the threeyear simulation were used 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 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. © 2015 by the article author(s). Source


Bever A.J.,Virginia Institute of Marine Science | Bever A.J.,Delta Modeling Associates Inc. | Friedrichs M.A.M.,Virginia Institute of Marine Science | Friedrichs C.T.,Virginia Institute of Marine Science | And 2 more authors.
Journal of Geophysical Research: Oceans | Year: 2013

The overall size of the "dead zone" within the main stem of the Chesapeake Bay and its tidal tributaries is quantified by the hypoxic volume (HV), the volume of water with dissolved oxygen (DO) less than 2 mg/L. To improve estimates of HV, DO was subsampled from the output of 3-D model hindcasts at times/locations matching the set of 2004-2005 stations monitored by the Chesapeake Bay Program. The resulting station profiles were interpolated to produce bay-wide estimates of HV in a manner consistent with nonsynoptic, cruise-based estimates. Interpolations of the same stations sampled synoptically, as well as multiple other combinations of station profiles, were examined in order to quantify uncertainties associated with interpolating HV from observed profiles. The potential uncertainty in summer HV estimates resulting from profiles being collected over 2 weeks rather than synoptically averaged ∼5 km3. This is larger than that due to sampling at discrete stations and interpolating/extrapolating to the entire Chesapeake Bay (2.4 km3). As a result, sampling fewer, selected stations over a shorter time period is likely to reduce uncertainties associated with interpolating HV from observed profiles. A function was derived that when applied to a subset of 13 stations, significantly improved estimates of HV. Finally, multiple metrics for quantifying bay-wide hypoxia were examined, and cumulative hypoxic volume was determined to be particularly useful, as a result of its insensitivity to temporal errors and climate change. A final product of this analysis is a nearly three-decade time series of improved estimates of HV for Chesapeake Bay. © 2013. The Authors. Journal of Geophysical Research: Oceans published by Wiley on behalf of the American Geophysical Union. Source


Bever A.J.,Delta Modeling Associates Inc. | MacWilliams M.L.,Delta Modeling Associates Inc.
Marine Geology | Year: 2013

San Pablo Bay is a tidal sub-embayment of the San Francisco Estuary which is dominated by broad shallow shoals bisected by a deep channel. Under the conceptual model of sediment transport in San Pablo Bay proposed by Krone (1979), sediment typically enters San Pablo Bay during large winter and spring flows and is redistributed during summer conditions through wind wave resuspension and transport by tidal currents. Numerical simulations of sediment resuspension due to wind waves and the subsequent transport of this sediment by tidal currents show that sediment concentrations and fluxes throughout the channel-shoal system result from a complex temporal and spatial interaction of the waves and tides. The three-dimensional UnTRIM San Francisco Bay-Delta Model was coupled with the Simulating WAves Nearshore (SWAN) wave model and the SediMorph morphological model, to develop a three-dimensional (3D) hydrodynamic, wind wave, and sediment transport model of San Francisco Bay and the Sacramento-San Joaquin Delta. The coupled model was validated using water level, velocity, wind waves and suspended sediment data collected in San Pablo Bay, and then used to quantify the spatial and temporal variability of sediment fluxes on the extensive shoals in San Pablo Bay under a range of tidal and wind conditions. The model validation shows this modeling system can accurately predict hydrodynamics, waves, and suspended sediment concentration in San Pablo Bay. The predicted bottom orbital velocities are elevated across the shoals during large wave events regardless of tidal stage, but near low tide orbital velocities are increased even under low to moderate waves. Sediment fluxes between the shoals and the deeper channel are highest during spring tides, and are elevated for up to a week following wave events, even though the greatest influence of the wave event occurs abruptly. © 2013 Elsevier B.V. Source

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