Hydrodynamics and sediment transport under time-varying boundary conditions at Baltimore Harbor mouth are simulated using a three-dimensional model. The model predictions are compared to those produced by constant monthly-averaged salinity and sediment boundary conditions and observational data at sampling sites. For monthly average values, both model predictions are compared reasonably with observations. For short-term predictions, the model results under time-varying boundary conditions have more variability than those under constant boundary conditions, as expected. However, time-varying boundary conditions do not improve the short-term predictions significantly and much of the variability that appears in the observational data is not captured. This behavior is partially because the time-varying salinity and sediment boundary conditions are derived from CH3D model output instead of real data.