The Manila Bay Area (MBA) plays an important role in the country’s economy. It supports major economic activities in terms of industry and commerce, agriculture, aquaculture, and tourism. The area hosts communities along the bay’s coasts and riverine areas, upland and lowland agricultural and forested fields, and rural and urban centers. However, due to the rapid urbanization and industrialization, the MBA and its resources are dwindling at a rapid rate. Environmental hazards are also triggered by the changing climate, thus exposing the communities to greater risk. These challenges call for a comprehensive plan backed with science-based policies in the management and rehabilitation of Manila Bay.