The Massachusetts Water Resources Authority's harbor and river monitoring program is designed to monitor the impacts of combined sewer overflows (CSOs) on tributary rivers and the Harbor. MWRA's sampling crew measures temperature, bacteria, algae, water clarity, dissolved oxygen, nutrients, and suspended solids in Boston Harbor and the Charles, Mystic, and Neponset rivers.

Bacterial counts in the Mystic River vary greatly depending on location. A tributary, Alewife Brook, is one of the most contaminated water bodies in the Boston area, mostly due to stormwater. Here, fecal coliform counts routinely fail to meet the state standard. However, bacterial water quality is fairly good downstream, except for a noticeable increase near Medford Square. water quality improves near the river’s mouth.