[1] The velocity reversal hypothesis is commonly cited as a mechanism for the maintenance of pool-riffle morphology. Although this hypothesis is based on the magnitude of mean flow parameters, recent studies have suggested that mean parameters are not sufficient to explain the dominant processes in many pool-riffle sequences. In this study, two-and three-dimensional models are applied to simulate flow in the pool-riffle sequence on Dry Creek, California, where the velocity reversal hypothesis was first proposed. These simulations provide an opportunity to evaluate the hydrodynamics underlying the observed reversals in near-bed and section-averaged velocity and are used to investigate the influence of secondary currents, the advection of momentum, and cross-stream flow variability. The simulation results support the occurrence of a reversal in mean velocity and mean shear stress with increasing discharge. However, the results indicate that the effects of flow convergence due to an upstream constriction and the routing of flow through the system are more significant in influencing pool-riffle morphology than the occurrence of a mean velocity reversal. The hypothesis of flow convergence routing is introduced as a more meaningful explanation of the mechanisms acting to maintain pool-riffle morphology.

Abundance of estuarine biota can vary with freshwater inflow through several mechanisms. One proposed mechanism is that the extent of physical habitat for an estuarine species increases with flow. We estimated the contribution of variation in habitat volume to the responses of eight species of estuarine nekton to changes in freshwater flow in the San Francisco Estuary. Resource selection functions for salinity and depth were developed for each species (and for five additional species) using five monitoring data sets. The TRIM3D hydrodynamic model was run for five steady flow scenarios to determine volume by salinity and depth, and resource selection functions were used as a weighting factor to calculate an index of total habitat for each species at each flow. The slopes of these habitat indices vs. flow were consistent with slopes of abundance vs. flow for only two of the species examined. Therefore, other mechanisms must underlie responses of abundance to flow for most species.

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.

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