Because of Boston's proximity to water, Bostonians historically diverted wastewater into the Charles River and the Boston Harbor. It wasn't until 1877 that Boston began constructing it's first official sewer system. According to the Massachusetts Water Resources Authority, the Boston Main Drainage System (BMDS) "diverted sewage from 18 cities and town to Moon Island in Boston Harbor. There sewage was held for release with the outgoing tide."
Presently, the Boston Water and Sewer Commission serves 70% of the total land area of Boston and uses two types of wastewater collection systems: Separate and combined sewer systems. Separate sewer systems separate sanitary waste and stormwater flow. Combined sewer systems combine sanitary waste and stormwater flow.
According to BWSC, the sewer system is approximately "1,455 linear miles, the sewer system consists of: 622 miles of sanitary, 595 miles of storm drain, 235 miles of combined sewer, and 3 miles of combined sewer overflow. The sewers are made of stone, brick, vitrified clay, concrete, iron, and cast iron. Vitrified clay is the most prevalent type of sewer material in the system because it has been used for some time as the standard material for the smaller diameter piping which is predominant in the system. Brick is the most common material for the larger pipes in the system because it was the principal building material used for large pipe in the late 1800's. Most new sewers are made of concrete, polyvinyl chloride (PVC) plastic or ductile iron."
Boston wastewater is currently sent to the Deer Island Waste Water Treatment Plant where it is treated and then sent into the ocean. Deer Island is now recognizable for its egg shaped anaerobic digesters.
If you are interested in how the sewer system works, here's a diagram.
Read more about stormwater management.