This study, supported by the Challenge Program Water and Food (CPWF-Project 35), demonstrates the case of multiple-use of water through seasonal aquaculture interventions for improved rice–fish production systems in the Bangladesh floodplains. The project focused on community-based fish culture initiatives, increasingly adopted in the agro-ecological zones of the major floodplains of the Padma, Testa, and Brahmaputra basin. The productivity of water and fish is used as an indicator to explain this case. We hypothesize that seasonal aquaculture supported by the management of floodplains for multiple-use of water can significantly increase the productivity of rice–fish systems. Recognizing the need for innovative ways to manage human-dominated landscapes and climate-sensitive ecosystems such as floodplains, we have analysed seasonal aquaculture interventions along with local adaptation of water management strategies, including the consideration of groundwater mechanisms. The results, supported by quantitative analysis and qualitative arguments, demonstrate the significant contribution of seasonal aquaculture in improving the rice–fish production systems of the selected floodplain sites. This was achieved through the increased productivity of water and fish and the reduction of the risk posed by arsenic contamination. The study is also illustrative of the diversification in livelihood-generating activities to cope with the extended period of flooding cycle in the region. We highlight the value of multiple resource-use approaches to enhance the social and ecological resilience of floodplains, and the need to re-consider basin water management options to recognize the water requirements of other sources of food such as fish produced by capture fisheries and aquaculture.