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The Massachusetts Water Resources Authority (MWRA) conducts a comprehensive multidisciplinary monitoring program in Massachusetts Bay, Cape Cod Bay, and Boston Harbor to assess the environmental effects of a relocated secondary-treated effluent outfall. Through 2007, 8.7 years of baseline data and 7.3 years of postdiversion data (16 total years), including species level estimates of phytoplankton and zooplankton abundance, have been collected. MWRA's monitoring program and other studies make this region one of the most thoroughly studied and well-described marine systems in the world. The data show that the diversion of MWRA effluent from the harbor to the bay has decreased nutrients concentrations and improved water quality in the harbor (e.g., higher dissolved oxygen, lower chlorophyll). The diversion also resulted in an increase in dissolved inorganic nutrients (especially ammonium) in the vicinity of the bay outfall, but no obvious impacts such as increased biomass or decreased bottom water dissolved oxygen have been observed. Regional changes in phytoplankton and zooplankton unrelated to the diversion have been seen, and it is clear that the bays are closely connected both physically and ecologically with the greater Gulf of Maine. Direct responses to modifications of the nutrient field within a 10×10-km area centered near the midpoint of the 2-km long outfall diffuser in Massachusetts Bay (a.k.a. the nearfield) have not been seen in the plankton community. However, plankton variability in the bays has been linked to large regional to hemispheric scale (NAO) processes.

Between 1991 and 2000, Boston Harbor, a bayestuary in the northeast USA, experienced a decrease in loadings of total nitrogen (TN), total phosphorus (TP), and particulate organic carbon (PC) of between ∼80% and ∼90%. The average concentrations of TN and TP in the harbor water column were decreased in linear proportion to the loadings. The changes to the chlorophyll-a (chl-a), PC, and bottom water DO concentrations were curvilinear relative to the loadings, with larger changes at low than high loadings. For TN and TP, the starts of the decreases in concentrations coincided with the starts of the decreases in loadings. For the three variables that showed curvilinear responses, the starts of the changes lagged by 2 to 3 years the starts of the decreases in TN loadings. Total suspended solid concentrations and water clarity in the harbor were unchanged. The study shows that for systems such as Boston Harbor, decreases in nutrient loadings will have quite different effects depending on the base loadings to the system.