This article is based on the findings of the Global International Waters Assessment (GIWA) Subregion 53, Bay of Bengal. It introduces the Subregion. The wide disparity in development indicators in the Bay of Bengal Subregion (BOBSR) is presented. The large population of poor people living in South Asia is presented as a factor that needs special attention. The article focuses on the 3 geographic sites selected for detailed analysis: i) the Ganges-Brahmaputra-Meghna river systems; ii) the Merbok Estuary mangroves, Malaysia; and iii) the Sunderbans mangroves, Bangladesh. Integrated water management based upon regional cooperation among Bangladesh, India and Nepal holds opportunities for mutual benefit. Policy options are proposed. For mangrove ecosystems, the impacts of urbanization in Malaysia and the unmanaged expansion of shrimp farming in Bangladesh are analyzed. Improved governance was seen to hold promise for enhancing economic benefits from shrimp farming while safeguarding the natural ecological system. However, these measures need to be a part of national efforts to achieve the UN Millennium Development Goals.