Estuarine aquatic systems and braided rivers in and adjacent to the Sundarbans and the vast area of the Ganges tidal floodplain next to the core forest area in Bangladesh holds rice aquatic faunal diversity and provides plenty of opportunities to grow fish, shrimps and crabs. Currently these systems provide direct employment opportunity for 1.2 million people and indirect or seasonal livelihood for more than 10 million people across the southwest coast. Hilsa is the largest fishery in this region and shrimp brings the highest cash and export earnings. Proper implementation of fisheries regulation is critical to ensure conservation of the rich fish diversity of this region as well as to continue to support livelihood of millions of people living on fisheries. While aquaculture is the major contributor to national fish production, agricultural GDP and export earning, it requires planned advancement from the current state to continue to grow in harmony with environment. Integration with rice and other crops, and with mangrove wherever possible can bring long-term sustainability of these systems. Change in the river flow due to siltation and reduced upstream flow, climate change, sea level rise, outbreak of disease in fish and crustaceans are major challenges for future growth and sustainability of both aquaculture and fisheries in this region. Collaborative and multi-disciplinary research should be undertaken to address these challenges. In addition, there should be mechanism to bring research outputs into use and make impact on sustainability.