In the 1980's, Boston Harbor was considered one of the filthiest in the nation. The pollution problem stemmed from the antiquated sewage treatment facility located on Deer Island, which discharged approximately 138 tons of wastewater solids and sludge just one-half mile offshore into the harbor every day. 
City of Boston from the harbor

In 1982, the City of Quincy and the U.S. Environmental Protection Agency (EPA) filed suit against the Commonwealth of Massachusetts for violations of the Clean Water Act in Boston Harbor, and won. 

The Massachusetts Bays Program (MassBays) was launched in 1988 as a result of the settlement fines from this lawsuit. That same year, MassBays was nominated into the United States National Estuary Program (NEP) , and was officially accepted in 1990. The National Estuary Program is sponsored by the EPA to identify nationally-significant estuaries threatened by pollution, development, or overuse, and create comprehensive management plans to ensure their ecological integrity. MassBays is one of 28 NEPs in the United States and is administered by the Massachusetts Coastal Zone Management Office (MCZM) .

In the early years of the program, MassBays conducted a major scientific research initiative to determine specific pollution problems in the Bays. At the same time, a Management Conference was convened to provide a forum for open discussion and collaborative decision-making. The Conference included nearly 300 representatives from federal, state, and local government agencies, regional planning agencies, various user groups, public and private institutions, and the general public.

These individuals were organized into a network of committees which collaboratively oversaw the activities and research of MassBays. Based on the research results, the Comprehensive Conservation and Management Plan (CCMP) was developed. The original CCMP was finalized in 1996, and contained 15 major Action Plans with 72 specific Action Items. Since the original drafting the CCMP has been updated with new initiatives and Action Plans. The CCMP serves as a blueprint for coordinated action among all levels of government to restore and protect the diverse natural resources of the Bays. The initial focus of MassBays has shifted from scientific research gathering and planning to CCMP implementation. And the Management Conference and associated committees have also evolved into the MassBays Management Committee, the group which oversees MassBays.