The Coalition for Buzzards Bay was officially incorporated in July 1987, as a nonprofit 501(c)(3) organization with start-up funding support from the US Environmental Protection Agency. The initial Board of Directors was comprised of individuals from throughout the Bay watershed - environmental advocates, cranberry growers, marina owners, research institutions and town government. Today, the organization continues to maintain a governing Board of private citizens concerned with the health and future of the Bay from Westport to Woods Hole and from a variety of backgrounds.

The push to reverse the decline of Bay water quality, shellfish beds, and wildlife populations had begun in earnest in 1984 when Congress recognized the unique value of Buzzards Bay by selecting the Bay as one of four estuaries in the country (Buzzards Bay in Massachusetts, Narragansett Bay in Rhode Island, San Francisco Bay in California, and Puget Sound in Washington) to be studied under the new National Estuary Program. With this program, a new government partnership between the US Environmental Protection Agency (EPA) and the Massachusetts Executive Office of Environmental Affairs (EOEA) was formed to create the Buzzards Bay Project (BBP). The objective of the BBP was to study water quality and living resources in the Bay, to assess threats to Bay health, and to develop a long-term management plan for the Bay. Toward that end, the Buzzards Bay Project completed a Comprehensive Conservation and Management Plan for the Bay in 1991.

Directing the activities of the BBP during its early years was a Citizens Advisory Committee (CAC) comprised of local town officials, environmental advocates, and members of the scientific community. This group was charged among other things with determining if Buzzards Bay would benefit from the establishment of a private advocate/watchdog group to insure that the right decisions were being made for the Bay long after the Buzzards Bay National Estuary Program was dissolved. In order to make that decision, the first Buzzards Bay Day was held on October 11, 1986 with varying events held around the Bay watershed - tours of Buttermilk Bay, the Elizabeth Islands, and the Pocasset River as well as clean-up projects in New Bedford and elsewhere. Ninety nine percent of the general public that came out for this first-of-its-kind regional event responded to a questionnaire that they felt that a permanent advocacy group was needed for Buzzards Bay. The Coalition for Buzzards Bay was formed less than a year later.