Muddy bottom sediments in industrialized coastal areas are often quite enriched in contaminants and organic matter. It is important to study the processes that control fine sediment accumulation in these areas. In order to examine the relationship between hydrodynamic forcing and sediment characteristics in Baltimore Harbor, MD, USA, estimated wave-induced bottom shear stresses were compared with sediment mud content distributions. Wave fields in the harbor were simulated with a numerical wave hindcasting model, HISWA. Spatial distributions of expected wave-induced bottom shear stresses in four wind speed ranges were obtained by directionally averaging wave-induced bottom shear stress predictions, weighting each direction by its probability of occurrence based on wind statistics from a long term data set collected near the harbor. A negative relationship between mud content and wave-induced shear stress was clear only for the stronger wind cases that occurred less than 5% of the time. The results suggest that the distribution of muddy bottom sediments in the mainstem of Baltimore Harbor is controlled largely by high wind wave events that occur infrequently.