The erodibility of cohesive sediment is known to vary both spatially and temporally but the factors governing its variation are not well understood. We conducted a field investigation of the influence of hydrodynamic forcing, sediment properties, and benthic infauna on erodibility in the muddy shallows of San Pablo and Grizzly Bays in northern San Francisco Bay in summer 2019 and winter 2020. An erosion rate parameter M_c was determined from regressions between near-bed vertical turbulent sediment flux, as a proxy for erosion, and bed shear stress due to currents. During each 2-month study period, we measured benthic infauna abundance and dry bulk density, particle size distribution, percent organic carbon, chlorophyll a, pheophytin a, and carbohydrates carbon concentrations of surficial bed sediments five or six times. M_c increased with bed shear stress due to waves in both embayments. In San Pablo Bay, erodibility was approximately 50% lower during the winter than the summer deployment, whereas in Grizzly Bay, there was no significant difference. The factor most strongly related to the decrease in M_c in San Pablo Bay was increased abundance of the amphipod Ampelisca abdita. The observed reduction in erodibility may occur in many muddy estuaries because A. abdita is broadly distributed in the coastal waters of North America. Erodibility was also directly related to biomass of the invasive clam Potamocorbula amurensis. Erodibility did not depend on dry bulk density: bulk density did not vary seasonally in San Pablo Bay and was lower in winter than summer in Grizzly Bay.