Computer models are an important tool that we can use to learn about the San Francisco Estuary. The San Francisco Estuary is a complex environment where salty water from the Pacific Ocean mixes with freshwater from rivers, because of tides, wind, and waves. These physical processes can be described using mathematical equations, which can be solved using computers. Using these equations to represent conditions in the San Francisco Estuary and solving them is called hydrodynamic modeling. Modeling of conditions in the Estuary requires an understanding of physics, mathematics, and computer science, which are combined to help us learn about the processes and environments in the Estuary. Models can be used to predict flooding and to design levees. They can also be used to help us improve how we manage the Estuary to provide a reliable water supply and to protect habitats for plants and animals.

While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed flow pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River flow into its adjacent Yolo Bypass floodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH₄, PO₄]) varied across the study region, and showed a strong response to the flow pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the flow pulse. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.

The sustained production of sufficient forage is critical to advancing ecosystem-based management, yet factors that affect local abundances and habitat conditions necessary to support aggregate forage production remain largely unexplored. We quantified suitable habitat in the Chesapeake Bay and its tidal tributaries for four key forage fishes: juvenile spotted hake Urophycis regia , juvenile spot Leiostomus xanthurus , juvenile weakfish Cynoscion regalis , and bay anchovy Anchoa mitchilli . We used information from monthly fisheries surveys from 2000 to 2016 coupled with hindcasts from a spatially interpolated model of dissolved oxygen and a 3-D hydrodynamic model of the Chesapeake Bay to identify influential covariates and construct habitat suitability models for each species. Suitable habitat conditions resulted from a complex interplay between water quality and geophysical properties of the environment and varied among species. Habitat suitability indices ranging between 0 (poor) and 1 (superior) were used to estimate seasonal and annual extents of suitable habitats. Seasonal variations in suitable habitat extents in Chesapeake Bay, which were more pronounced than annual variations during 2000–2016, reflected the phenology of estuarine use by these species. Areas near shorelines served as suitable habitats in spring for juvenile spot and in summer for juvenile weakfish, indicating the importance of these shallow areas for production. Tributaries were more suitable for bay anchovy in spring than during other seasons. The relative baywide abundances of juvenile spot and bay anchovy were significantly related to the extent of suitable habitats in summer and winter, respectively, indicating that Chesapeake Bay habitats may be limiting for these species. In contrast, the relative baywide abundances of juvenile weakfish and juvenile spotted hake varied independently of the spatial extent of suitable habitats. In an ecosystem-based approach, areas that persistently provide suitable conditions for forage species such as shoreline and tributary habitats may be targeted for protection or restoration, thereby promoting sufficient production of forage for predators. Further, quantitative habitat targets or spatial thresholds may be developed for habitat-limited species using estimates of the minimum habitat area required to produce a desired abundance or biomass; such targets or thresholds may serve as spatial reference points for management.

Delta Smelt, Hypomesus transpacificus, is an endangered pelagic fish native to the San Francisco Estuary. The distribution of Delta Smelt in the estuary shifts landward from low-salinity habitat to freshwater habitat before spawning. This spawning migration often coincides with the first substantial freshwater inflow to the estuary during winter. To accomplish this landward shift in distribution, Delta Smelt are believed to use the tides by swimming to faster-moving currents during flood tides and then repositioning themselves to slower-moving currents to reduce seaward movement on ebb tides. Studies have hypothesized that the swimming behavior of Delta Smelt during this period is influenced by environmental conditions such as salinity and turbidity. The details of these swimming behaviors—including the extent to which flows, salinity, and turbidity affect behaviors and distributions—are uncertain. The spawning migration is of management interest because an increase in observed counts of Delta Smelt at the South Delta water-export facilities has coincided roughly with the spawning migration in many years. In this study, we investigated a range of hypothesized swimming behaviors using a three-dimensional particle-tracking model for water year 2002 during the spawning migration, and compared the predicted distributions of Delta Smelt to distributions inferred from catch data. Our goal was to improve understanding of the influence of Delta Smelt swimming on distribution, and, ultimately, to develop a modeling tool to help management agencies identify conditions associated with entrainment losses. Predictions of Delta Smelt distributions and entrainment varied greatly among behaviors. Without swimming, Delta Smelt would be rapidly transported seaward of Suisun Bay, while continuous tidal migration would move them deep into the interior Delta. These behaviors and a simple turbidity-driven behavior model predicted distributions inconsistent with observations, while more complex behavior rules allowed improved predictions.

While flow is known to be a major driver of estuarine ecosystems, targeted flow manipulations are rare because tidal systems are extremely variable in space and time, and because the necessary infrastructure is rarely available. In summer 2018 we used a unique water control structure in the San Francisco Estuary (SFE) to direct a managed flow pulse into Suisun Marsh, one of the largest contiguous tidal marshes on the west coast of the United States. The action was designed to increase habitat suitability for the endangered Delta Smelt Hypomesus transpacificus, a small osmerid fish endemic to the upper SFE. The approach was to operate the Suisun Marsh Salinity Control Gates (SMSCG) in conjunction with increased Sacramento River tributary inflow to direct an estimated 160 x 106 m3 pulse of low salinity water into Suisun Marsh during August, a critical time period for juvenile Delta Smelt rearing. Three-dimensional modeling showed that directing additional low salinity water into Suisun Marsh ("Flow Action") substantially increased the area of low salinity habitat for Delta Smelt that persisted beyond the period of SMSCG operations. Field monitoring showed that turbidity and chlorophyll were at higher levels in Suisun Marsh, representing better habitat conditions, than the upstream Sacramento River region throughout the study period. The Flow Action had no substantial effects on zooplankton abundance, nor did Suisun Marsh show enhanced levels of these prey species in comparison to the Sacramento River. Fish monitoring data suggested that small numbers of Delta Smelt colonized Suisun Marsh from the Sacramento River during the 2018 Flow Action. Comparison of the salinity effects of the Flow Action to historical catch data for Suisun Marsh further supported our hypothesis that the Flow Action would have some benefit for this rare species. Our study provides insight into both the potential use of targeted flow manipulations to support endangered fishes such as Delta Smelt, and into the general response of estuarine habitat to flow management.

Turbidity is an important habitat component in estuaries for many fishes and affects a range of other ecological functions. Decadal timescale declines in turbidity have been observed in the San Francisco Estuary (Estuary), with the declines generally attributed to a reduction in sediment supply to the Estuary and changes to the erodible sediment pool in the Estuary. However, we analyzed hourly wind data from 1995 through 2015 and found statistically significant declines of 13 to 48% in wind speed around the Estuary. This study applied a 3-D hydrodynamic, wave, and sediment transport model to evaluate the effects of the observed decrease in wind speed on turbidity in the Estuary. The reduction in wind speed over the past 20years was predicted to result in a decrease in turbidity of 14 to 55% in Suisun Bay from October through January. These results highlight that the observed declines in both wind speed and sediment supply over the past 20years have resulted in reduced turbidity in the San Francisco Estuary from October through January. This decline in turbidity in Suisun Bay potentially has negative effects on habitat for fish like the endangered Delta Smelt which are more commonly caught in relatively turbid water.

Author(s): Bever, Aaron J.; MacWilliams, Michael L.; Herbold, Bruce; Brown, Larry R.; Feyrer, Frederick V. | Abstract: Long-term fish sampling data from the San Francisco Estuary were combined with detailed three-dimensional hydrodynamic modeling to investigate the relationship between historical fish catch and hydrodynamic complexity. Delta Smelt catch data at 45 stations from the Fall Midwater Trawl (FMWT) survey in the vicinity of Suisun Bay were used to develop a quantitative catch-based station index. This index was used to rank stations based on historical Delta Smelt catch. The correlations between historical Delta Smelt catch and 35 quantitative metrics of environmental complexity were evaluated at each station. Eight metrics of environmental conditions were derived from FMWT data and 27 metrics were derived from model predictions at each FMWT station. To relate the station index to conceptual models of Delta Smelt habitat, the metrics were used to predict the station ranking based on the quantified environmental conditions. Salinity, current speed, and turbidity metrics were used to predict the relative ranking of each station for Delta Smelt catch. Including a measure of the current speed at each station improved predictions of the historical ranking for Delta Smelt catch relative to similar predictions made using only salinity and turbidity. Current speed was also found to be a better predictor of historical Delta Smelt catch than water depth. The quantitative approach developed using the FMWT data was validated using the Delta Smelt catch data from the San Francisco Bay Study. Complexity metrics in Suisun Bay were evaluated during 2010 and 2011. This analysis indicated that a key to historical Delta Smelt catch is the overlap of low salinity, low maximum velocity, and low Secchi depth regions. This overlap occurred in Suisun Bay during 2011, and may have contributed to higher Delta Smelt abundance in 2011 than in 2010 when the favorable ranges of the metrics did not overlap in Suisun Bay.

Multi-spectral satellite images of the San Francisco Bay region have the potential to provide broad spatial information about biological productivity, water quality, suspended particulate matter (SPM), and light attenuation. While satellite remote sensing algorithms are well established for quantification of sea-surface temperature and biological productivity in the ocean, there is currently very little remote sensing work designed to predict SPM in estuaries like San Francisco Bay. As part of a project in which we seek to deploy UAVs with high-resolution, multispectral cameras to measure surface SPM, we have developed algorithms to infer surface SPM in San Francisco Bay from Landsat Enhanced Thematic Mapper Plus data and validated the results with USGS Polaris cruise measurements. We tested several regression algorithms including: linear regression, Huber regression, and an artificial neural network. Neural networks are a class of machine learning algorithms well suited to non-linear statistical modeling. Our calibrated neural network best reconstructed a reserved testing set of in situ SPM measurements with an R value of 0.76. Although the Huber regression—an alternative to linear regression that is robust against outliers—did not predict SPM concentrations as well as the neural network (R = 0.74), it is a recommended alternative, because it possesses the attractive quality of being a linear equation that is straightforward to understand without sacrificing a large amount of performance. Therefore, we have implemented the Huber regression on a series of satellite images and used it to estimate surface SPM concentrations throughout San Francisco Bay.

Over the past 15 years, the development and application of multi-dimensional hydrodynamic models in San Francisco Bay and the Sacramento– San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta under future conditions. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship among X2, flow, fish abundance, and the low salinity zone. Through the coupling of multi-dimensional models with wind wave and sediment transport models, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms in the estuary, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This paper provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multi-dimensional models to predict how future Delta conditions will affect both fish and water supply.

doi: http://dx.doi.org/10.15447/sfews.2016v14iss2art3The UnTRIM hydrodynamic model was applied to San Francisco Bay and the Sacramento–San Joaquin Delta (Delta) using a coarse-resolution model grid with bathymetry represented at a finer subgrid scale. We simulated a 35-year period, spanning from January 1, 1980 through December 31, 2014. This simulation was used to develop salinity distribution maps to facilitate visualization of fish distribution and abundance data. We compared predicted salinity from the coarse-grid UnTRIM Bay–Delta model to continuous salinity monitoring observations as well to the measured surface salinity from San Pablo Bay through the Delta at a total of 5,542 times and locations where surface salinity was observed as part of several long-term fish monitoring programs: the Fall Midwater Trawl, Summer Townet Survey, and San Francisco Bay Study. The coarse-grid UnTRIM Bay–Delta model was shown to accurately predict hydrodynamics and the spatial distribution of salinity over both a 3-year detailed validation period and over the full 35-year analysis period. The predicted salinity was used to calculate the daily position of X2 and the daily-averaged area of the Low Salinity Zone (LSZ) for each day during the 35-year simulation. Our analysis highlights the influence of multi-year climate patterns, shorter-duration weather patterns, and Delta outflow on salinity distribution. We used the predicted salinity to develop maps of salinity distribution over seven periods for six fish species, and combined the salinity maps with historic fish sampling data to allow for visualization of fish abundance and distribution for 33 years between 1980 and 2012. These maps can be used to explore how different species respond to annual differences in salinity distributions in the San Francisco Estuary, and to expand the understanding of the relationships among salinity and fish abundance, distribution, and population resiliency.

doi: http://dx.doi.org/10.15447/sfews.2015v13iss1art2The 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.

Secondary circulation is the component of three-dimensional (3D) flow in river channels perpendicular to the primary flow direction. Secondary circulation calculated from acoustic Doppler current profiler (ADCP) transects is sensitive to the calculation method and is affected by the transect angle relative to the mean flow direction and variations in the flow direction along a transect. To quantify bounds on transect alignment relative to river flow for field data collection and examine tidal time-scale variability in secondary circulation, the 3D hydrodynamic model UnTRIM was applied to simulate the hydrodynamics in the lower reach of the Sacramento River (CA, USA). Secondary circulation was calculated using the Rozovskii and the zero net discharge methods on repeated transects extracted from the model results in regions of both relatively uniform and complex flows. When the depth-averaged flow direction along a transect varied by more than about 5 degrees, occurring when the transect was as little as 10 to 20 degrees out of normal to the mean flow direction, the Rozovskii method produced more realistic secondary circulation than the zero net discharge method. Analysis indicated that ADCP transects should be within 20 degrees of perpendicular to the mean flow direction when calculating secondary circulation. Secondary circulation strength around two tidally influenced bends generally increased with increasing flow and broke down near slack water. However, the strength of the secondary circulation was not only a function of the flow magnitude, but also depended on the direction of the water flow and the transect location relative to the river curvature, which varied with the tidal flow direction. Copyright (c) 2015 John Wiley & Sons, Ltd.

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. Volume 13, Issue 1 | April 2015 doi: http://dx.doi.org/10.15447/sfews.2015v13iss1art2 * Corresponding author: michael@deltamodeling.com 1 Delta Modeling Associates, Inc., 870 Market Street, Suite 1074, San Francisco, CA 94102 USA 2 Resource Management Associates, Inc., Berkeley, CA 94704 USA 3 Romberg Tiburon Center, San Francisco State University, Tiburon CA 94920 USA Three-Dimensional Modeling of Hydrodynamics and Salinity in the San Francisco Estuary: An Evaluation of Model Accuracy, X2, and the Low-Salinity Zone Michael L. MacWilliams*1, Aaron J. Bever1, Edward S. Gross2, Gerard S. Ketefian2, and Wim J. Kimmerer3 SAN FRANCISCO ESTUARY & WATERSHED SCIENCE

We used hydrodynamic and particle‐tracking models to investigate vertical movement of plankton and resulting retention in the San Francisco Estuary. The hydrodynamic model was UnTRIM, a three‐dimensional, unstructured grid model, which had been calibrated to historical conditions in this estuary for 1994–1997, a period of widely varying hydrology. Intensive field studies of hydrodynamics and vertical movements of organisms during 1994–1996 provided input data for the models. The particle‐tracking model was run with 14 alternative behaviors for three 45 d periods of contrasting hydrology. The behaviors included passive behavior, several simple tidal migration patterns, and several sinking speeds. Vertical positions of migrating and sinking particles resembled those seen in the field studies for copepods and epibenthos, respectively. Passive particles were advected from the estuary at rates that depended on freshwater flow. All of the non‐passive behaviors caused retention of the particles in the low‐salinity region of the estuary under some flow conditions. Tidal migration was very effective at maintaining position, but model results and a re‐examination of the field data suggested that migration speed should increase with increasing freshwater flow. Continuous sinking was also effective at retention, particularly in deep areas of low tidal velocity. We conclude that the vertical distributions observed in the field studies were a result of active patterns of movement, that these patterns can result in retention, and that retention in a bathymetrically complex estuary can be understood only in the context of the full time‐varying three‐dimensional flow field.

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 near-bottom 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 up-dated 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.

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.