Southern Asia benefits from groundwater pumping for dry-season irrigation by increasing both crop productivity and monsoon aquifer recharge rates in the region. Based on a data-driven integrated modeling system, we provide numerical evidence that the impacts of unsustainable groundwater-fed irrigation surface freshwater availability go beyond what was previously understood. Our results confirm findings from previous studies that increased groundwater recharge rates during wet seasons over 2002-2021, but they are insufficient for aquifers to recover, gradually depleting groundwater across the Ganges-Brahmaputra-Meghna delta. Main findings are that such an increased recharge causes a drop in runoff generation during the monsoons, resulting in lower flood risk, a good outcome, but also less surface freshwater available for farming, which may trigger additional groundwater demand during monsoons. Drop in coastal flooding induced by groundwater-fed irrigation exceeds by ~5-10 fold the flooding increase caused by sea level rise. Reduced runoff also increases seawater intrusion, driven by less freshwater to push ocean water away. This is particularly concerning, since the region has been under rising sea levels and sinking lands. These findings over this delta have global implications, as humans and climate are increasingly pressuring coastal and deltaic ecosystems worldwide.