Water supply to the world’s megacities is a problem of quantity and quality that will be a priority in the coming decades. Heavy pumping of groundwater beneath these urban centres, particularly in regions with low natural topographic gradients, such as deltas and floodplains, can fundamentally alter the hydrological system. These changes affect recharge area locations, which may shift closer to the city centre than before development, thereby increasing the potential for contamination. Hydrogeological simulation analysis allows evaluation of the impact on past, present and future pumping for the region of Kolkata, India, on recharge area locations in an aquifer that supplies water to over 13 million people. Relocated recharge areas are compared with known surface contamination sources, with a focus on sustainable management of this urban groundwater resource. The study highlights the impacts of pumping on water sources for long-term development of stressed city aquifers and for future water supply in deltaic and floodplain regions of the world.