Three-dimensional wave-coupled hydrodynamics modeling in South San Francisco Bay

In this paper, we present a numerical model to simulate wind waves and hydrodynamics in the estuary. We employ the unstructured-grid SUNTANS model for hydrodynamics, and within this model we implement a spectral wave model which solves for transport of wave action density with the finite-volume formulation. Hydrodynamics is coupled to the wave field through the radiation stress. Based on the unstructured grid and finite-volume formulation of SUNTANS, the radiation stress is implemented in a way that directly calculates the divergence of transport of the wave-induced orbital velocity. A coupled hydrodynamics–wave simulation of San Francisco Bay is then performed. Through the input of wind forcing that is obtained from the reconstructed wind field, the model is capable of predicting wave heights that are in good agreement with the field measurements. We examine the importance of modeling sea bed dissipation in muddy shallow water environments by using a bottom friction model and a bed mud model with different mud layer thicknesses. Moreover, currents driven by wave shoaling and dissipation are investigated in the presence of abrupt bathymetric change. We find that spatially varying wave heights induced by spatially heterogeneous bottom mud dissipation produce wave-driven currents that are stronger than those induced by wave shoaling and can be of the same order as the tidal currents in shallow water. •An unstructured-grid model is presented to simulate hydrodynamics under wind-wave and tidal forcing.•Simulations are performed to study wave-coupled hydrodynamics in San Francisco Bay.•Currents driven by waves are investigated in the presence of abrupt bathymetric change.