An 18 month simulation of circulation was conducted in Massachusetts Bay, a roughly 35 m deep, 100??50 km embayment on the northeastern shelf of the United States. Using a variant of the Blumberg-Mellor (1987) model, it was found that a continuous 18 month run was only possible if the velocity field was Shapiro filtered to remove two grid length energy that developed along the open boundary due to mismatch in locally generated and climatologically forced water properties. The seasonal development of temperature and salinity stratification was well-represented by the model once ??-coordinate errors were reduced by subtracting domain averaged vertical profiles of temperature, salinity and density before horizontal differencing was performed. Comparison of modeled and observed subtidal currents at fixed locations revealed that the model performance varies strongly with season and distance from the open boundaries. The model performs best during unstratified conditions, and in the interior of the bay. The model performs poorest during stratified conditions and in the regions where the bay is driven predominantly by remote fluctuations from the Gulf of Maine.