A time-dependent, three-dimensional numerical modeling study of the tides of Massachusetts and Cape Code Bays, motivated by construction of a new sewage treatment plant and ocean outfall for the city of Boston, has been undertaken by the authors. The numerical model being used is a hybrid version of the Blumberg and Mellor ECOM3D model, modified to include a semi-implicit time-stepping scheme and transport of a non-reactive dissolved constituent. Tides in the bays are dominated by the semi-diurnal frequencies, in particular by the M2 tide, due to the resonance of these frequencies in the Gulf of Maine. The numerical model reproduces, well, measured tidal ellipses in unstratified wintertime conditions. Stratified conditions present more of a problem because tidal-frequency internal wave generation and propagation significantly complicates the structure of the resulting tidal field. Nonetheless, the numerical model reproduces qualitative aspects of the stratified tidal flow that are consistent with observations in the bays.