Understanding the spatio-temporal variability in groundwater recharge is a prerequisite to sustainable management of aquifers. Spatial analysis of groundwater stable isotopes uncovered predominant controls on groundwater recharge in the Nairobi aquifer system (NAS) and the South Coast aquifer (SC), two exemplar East African aquifers relied upon by 7 million people. We analysed 368 samples for stable isotopes and basic physico-chemical parameters. The NAS groundwater isotopes are controlled by precipitation orographic effects and enriched recharge from impounded lakes/wetlands; the SC isotopes are correlated with water-table depth influencing evapotranspiration. Global Network of Isotopes in Precipitation (GNIP) data revealed groundwater recharge during months of heavy rains in the NAS, whilst the SC experiences spatiotemporally diffuse recharge. Inferred "isoscapes" show: in the NAS, (1) direct, rapid recharge favoured by faults, well-drained soils and ample rainfall in uplands, (2) delayed recharge from impounded lakes and wetlands in mid-lands, and (3) focused, event-based recharge in floodplains; and in the SC, diffuse recharge complicated by significant water-table evapotranspiration processes.