We conducted field work on the shoals of South San Francisco Bay to elucidate the mechanisms driving cohesive sediment erosion in a shallow, wave- and current-driven flow. Compiling data from three deployments, including measurements taken within the combined wave-current boundary layer, we found that waves were strongly correlated to turbulent sediment fluxes across all seasons and a range of deployment depths. Tidal turbulence was only correlated to turbulent sediment fluxes for larger relative depths, or when a wave-driven sediment flux into the boundary layer allowed the tidal shear stress to transport sediment into the overlying flow. Despite the dominance of waves in eroding sediment, we found favorable agreement between in situ boundary layer erosion measurements and laboratory erosion measurements conducted in a steady flume. Results were analyzed in the context of two benthic surveys which provided insight into the sediment bed properties.