Simulating sediment transport processes in San Pablo Bay using coupled hydrodynamic, wave, and sediment transport models

• Coupled 3D hydrodynamic, wind wave and sediment model applied to San Francisco Bay.
• Model accurately predicts hydrodynamics, waves, and suspended sediment concentration.
• Sediment fluxes in the system result from a complex interaction of tides and waves.
• Including effect of wind waves on bed shear stress increased erosion rate on shoals.
• Wave height more sensitive than orbital velocity to water level during large waves.

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.