The Massachusetts Bays region covers over 800 miles of coastline, from the tip of Cape Cod Bay to the New Hampshire border, and serves 50 coastal communities. With such a large area to cover (MBP is one of the largest NEPs in the country), MBP devised an innovative staffing structure to ensure that each region would receive the attention it deserved. MBP has teamed up with three nonprofit organizations and one Regional Planning Agency based in coastal Massachusetts to host MBP staff members. As a result, MBP staff is working with communities to implement CCMP projects in five coastal subregions: Upper North Shore , Salem Sound , Metro Boston , South Shore , and Cape Cod .

These regional staff members lead Local Governance Committees (LGCs), which are comprised of appointed members from each coastal community within a subregion, including municipal officials, members of non-profit organizations, state and local governments, and the public at large. LGCs are responsible for identifying priority needs within the community and devising projects that implement CCMP goals. Through this close relationship with municipalities MBP is able to successfully complete projects and improve the overall health of the Bays.

MBP is governed by a Management Committee comprised of members of LGCs, CZM, EPA, and other partners. It meets three times a year along with MBP and MBEA staff. The Management Committee is accountable to the EPA Regional Administrator and the Secretary of the Executive Office of Energy and Environmental Affairs to carry out the charge of program implementation and make recommendations in accordance with its charge and applicable laws, ordinances and regulations.