Cohesive sediment modeling in a shallow estuary: Model and environmental implications of sediment parameter variation

Numerical models of sediment transport in estuarine systems rely on parameter values that are often poorly constrained and can vary on timescales relevant to model processes. The selection of parameter values can affect the accuracy of model predictions, while environmental variation of these parameters can impact the temporal and spatial ranges of sediment fluxes, erosion, and deposition in the real world. We implemented a numerical model of San Pablo Bay, an embayment within San Francisco Bay, California, for November–December 2014, and compared model outputs to observations of water level, velocity, wave parameters, salinity, and suspended sediment concentration (SSC) in the shallow regions. Idealized model runs show that wind timing relative to the phase of the tides is the strongest control on sediment fluxes and bed erosion. We varied sediment erodibility in the outflow of the Petaluma River; while this causes erosion and deposition to vary strongly through the shallows system, total export from the shallows does not change. Model runs with realistic winds show that wind likely resuspends faster settling particles or allows for more particle flocculation; particle settling velocity controls system-wide sediment accumulation. At the margins of the system, the magnitude of SSC is closely tied to wind direction when winds occur during flood tide, but sediment deposition is less connected: Both bed evolution and SSC need to be considered in the prediction of marsh fate. Spatial patterns of light attenuation due to SSC is strongly tied to assumed settling velocity.