E. coli and fecal coliform are bacteria found in human and animal waste, measured in recreational waters to indicate bacterial water quality and to assess public health risk. E. coli counts greater than 126 colonies per 100 milliliters of water fail to meet the Massachusetts Department of Public Health swimming standard and indicate poor water quality. High levels of E. coli can occur following heavy rains that carry untreated waste into rivers and the harbor from storm runoff and combined sewer overflows.

Microscopic plants, or phytoplankton, the overgrowth of which can degrade water quality. In the harbor and rivers, photosynthesis is carried out by algae (or phytoplankton), microscopic plants suspended in the water column. To determine the amount of algae in the water, we measure chlorophyll. High chlorophyll concentrations indicate an overabundance of nutrients in the water, which can result in elevated algae levels, or algal blooms. Algal blooms can deplete bottom-water dissolved oxygen, reduce water clarity, and impair recreational uses. Chlorophyll concentrations greater than 12 micrograms per liter in the Harbor and 25 micrograms per liter in the rivers indicate an overgrowth of algae.