Once per month, CRWA collects water samples from multiple sites along the entire length of the 80-mile Charles River. Prior to 2002, CRWA analyzed all samples for fecal coliform bacteria, however due to changes in water quality standards, CRWA now collects and analyzes samples for Escherichia coli , or E. coli, which serves as a better indicator of health risks. Previously, CRWA's laboratory analyzed samples for fecal coliform bacteria, which is one parameter used by the state for surface water quality standards.

According to the U.S. Environmental Protection Agency (EPA) and the Massachusetts Department of Environmental Protection (DEP), the swimming standard for E. coli is 126 colony forming units per 100 milliliters (cfu/100mL) and the boating standard is 630cfu/100mL.

The standards for fecal coliform are set by the Massachusetts Department of Environmental Protection to indicate level of health risk. The DEP recommends not swimming or fishing when bacteria counts exceed 200cfu/100mL, and not boating on days when levels rise above 1,000cfu/100mL.

In addition to collecting water samples which are analyzed for bacteria, CRWA measures temperature and depth on site on a monthly basis.

Every year in March, June, September, and December, CRWA takes a closer look at the water quality of the Charles River. In addition to testing for E. coli, CRWA tests for enterococci, nitrate plus nitrite, ammonia, total kjeldahl nitrogen, total nitrogen, phosphorus, orthophosphate, chlorophyll a, and phaeophytin. For more information the parameters CRWA tests for on a regular basis, read CRWA Water Quality Monitoring Parameters.