The 50 square miles encompassing the Boston Harbor estuary include tributary rivers mixing with the salt water of Massachusetts Bay. There are eight main watersheds that drain into Boston Harbor.

Boston Harbor clearly benefited from the Boston Harbor Project, which improved sewage treatment and moved wastewater treatment plant discharges from Boston Harbor to Massachusetts Bay.

The Massachusetts Water Resources Authority (MWRA) collects water quality data at more than 70 locations in the Harbor and its tributary rivers, data that can be downloaded from the water quality data page. The results show how Boston Harbor has steadily become cleaner since the effluent and solids discharges from treatment plants were removed.

MWRA and the Massachusetts Department of Conservation & Recreation also monitor several harbor beaches.