In the early years of the program, MBP 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 MBP. Based on the research results, the Comprehensive Conservation and Management Plan (CCMP) was developed. The CCMP was finalized in 1996, and contains 15 major Action Plans with 72 specific action items. 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. Because the initial focus of MBP has shifted from scientific research gathering and planning to CCMP implementation, the Management Conference and associated committees have also evolved into a Management Committee.