Our environment is heterogeneous. In hydrological sciences, the heterogeneity of subsurface properties, such as hydraulic conductivities or porosities, exerts an important control on water balance. This notably includes groundwater recharge, which is an important variable for efficient and sustainable groundwater resources management. Current large-scale hydrological models do not adequately consider this subsurface heterogeneity. Here we show that regions with strong subsurface heterogeneity have enhanced present and future recharge rates due to a different sensitivity of recharge to climate variability compared with regions with homogeneous subsurface properties. Our study domain comprises the carbonate rock regions of Europe, Northern Africa, and the Middle East, which cover ∼25% of the total land area. We compare the simulations of two large-scale hydrological models, one of them accounting for subsurface heterogeneity. Carbonate rock regions strongly exhibit “karstification,” which is known to produce particularly strong subsurface heterogeneity. Aquifers from these regions contribute up to half of the drinking water supply for some European countries. Our results suggest that water management for these regions cannot rely on most of the presently available projections of groundwater recharge because spatially variable storages and spatial concentration of recharge result in actual recharge rates that are up to four times larger for present conditions and changes up to five times larger for potential future conditions than previously estimated. These differences in recharge rates for strongly heterogeneous regions suggest a need for groundwater management strategies that are adapted to the fast transit of water from the surface to the aquifers.