<p>Southern Asia benefits from groundwater pumping for dry-season irrigation by increasing both crop productivity and monsoon aquifer recharge rates in the region. On the basis of a data-driven integrated modelling system, we provide numerical evidence that the impacts of unsustainable groundwater-fed irrigation on surface freshwater availability go beyond what was previously understood. Our results confirm findings from previous studies showing increased groundwater recharge rates during wet seasons over 2002–2021, but these rates are insufficient for aquifers to recover, gradually depleting groundwater across the Ganges–Brahmaputra–Meghna delta. The main findings are that this increased recharge causes a drop in surface runoff and baseflow generation during the monsoons, resulting in lower flood risk (a beneficial outcome), but also less surface freshwater available for farming, which may trigger additional groundwater demand. The drop in coastal flood risk induced by inland groundwater-fed irrigation exceeds the increase caused by sea level rise by about five- to tenfold. Reduced runoff may also increase seawater intrusion, driven by less freshwater to push ocean water away, further increasing freshwater scarcity. This is particularly concerning, since the region has been under rising sea levels and sinking lands. Our findings over this delta have global implications, as humans and climate are increasingly pressuring coastal and deltaic ecosystems worldwide.</p>