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Groundwater recharge sustains the groundwater resources on which there is global dependence for drinking water and irrigated agriculture1. For many communities, groundwater is the only perennial source of water. Here, we present a newly compiled 55-year record of groundwater-level observations in an aquifer of central Tanzania that reveals the highly episodic occurrence of recharge resulting from anomalously intense seasonal rainfall. Episodic recharge interrupts multiannual recessions in groundwater levels, maintaining the water security of the groundwater-dependent communities in this region. This long-term record of groundwater storage changes in the semi-arid tropics demonstrates a nonlinear relationship between rainfall and recharge wherein intense seasonal rainfall associated with the El Niño Southern Oscillation and the Indian Ocean Dipole mode of climate variability2,3 contributes disproportionately to recharge. Analysis of the Intergovernmental Panel on Climate Change AR4 and AR5 multi-model ensembles for the twenty-first century indicates that projected increases in extreme monthly rainfall, responsible for observed recharge, are of much greater magnitude than changes to mean rainfall. Increased use of groundwater may therefore prove a potentially viable adaptation to enhanced riability in surface-water resources and soil moisture resulting from climate change4–7. Uncertainty in the projected behaviour of the El Niño Southern Oscillation and associated teleconnections remains, however, high8.