We investigated the driving forces of sediment dynamics at the shoals in South San Francisco Bay. Two stations were deployed along a line perpendicular to a 14 m deep channel, 1000 and 2000 m from the middle of the channel. Station depths were 2.59 and 2.19 m below mean lower low water, respectively. We used acoustic Doppler velocimeters for the simultaneous determination of current velocities, turbulence, sediment concentration and fluxes. Maximum current shear velocities were 0.015 m s−1 at the station further from the channel (closer to the shore) and 0.02 m s−1 at the station closer to the channel. Peak wave-induced shear velocities exceeded 0.015 m s−1 at both stations. Maximum sediment concentrations were around 30 g m−3 during calm periods (root mean square wave height <0.15 m). During wavy periods, sediment concentrations increased to 100 g m−3 and sediment fluxes were 5 times higher than in calm conditions (0.02 g m−2 s−1 versus >0.10 g m−2 s−1) at the station further from the channel 0.36 m above the bed. Closer to the channel, sediment concentrations and vertical fluxes due to wind wave resuspension were persistently lower (maximum concentrations around 50 g m−3 and maximum fluxes around 0.04 g m−2 s−1). Most resuspension events occurred during flood tides that followed wave events during low water. Although wave motions are able to resuspend sediment into the wave boundary layer at low tide, the observed large increases in sediment fluxes are due to the nonlinear interaction of wind waves and the tidal currents.