The Massachusetts Water Resources Authority's harbor and river monitoring program monitors the impacts of combined sewer overflows (CSOs) on the Harbor and tributary rivers. The Environmental Quality Department (ENQUAD) manages water quality data collected over years of monitoring. The sampling crew measures temperature, bacteria, algae, water clarity, dissolved oxygen, nutrients, and suspended solids.

In the Charles, improvement in water quality over the past decade has been dramatic. Most fecal coliform bacteria counts do not exceed the state standard of 200 colonies per 100 milliliters. The area between the Watertown dam and the Arsenal Mall (upstream of any CSO discharges) is the most consistently contaminated section surveyed; and the Charles River Basin, the important recreational area between Cambridge and Boston, had the best bacterial water quality.