In shallow, fetch-limited estuaries, variations in current and wave energy promote heterogeneous surface water-groundwater mixing (benthic exchange), which influences biogeochemical activity. Here, we characterize heterogeneity in benthic exchange within the subtidal zone of the Delaware Inland Bays by linking hydrodynamic circulation models with mathematical solutions for benthic exchange forced by current-bedform interactions, tides, and waves. Benthic fluxes oscillate over tidal cycles as fluctuating water depths alter fluid interactions with the bed. Maximum current-driven fluxes (~1–10 cm/d) occur in channels with strong tidal currents. Maximum wave-driven fluxes (~1–10 cm/d) occur in downwind shoals. During high-energy storms, simulated wave pumping rates increase by orders of magnitude, demonstrating the importance of storms in solute transfer through the benthic layer. Under moderate wind conditions (~5 m/s), integrated benthic exchange rates due to wave, current, and tidal pumping are each ~1–10 m3/s, on the order of fluid contributions from runoff and fresh groundwater discharge to the estuary. Benthic exchange is thus a significant and dynamic component of an estuary's fluid budget that may influence estuarine geochemistry and ecology.