Little is known of the interactions between groundwater and surface water on deeply weathered landscapes of low relief in the Great Lakes Region of Africa (GLRA). The role of groundwater in sustaining surface-water levels during periods of absent rainfall is disputed and groundwater is commonly excluded from estimations of surface-water balances. Triangulated piezometers installed beside lake gauging stations on Lake Victoria and Lake Kyoga in Uganda provide the first evidence of the dynamic interaction between groundwater and surface water in the GLRA. Stable isotope ratios (2H:1H, 18O:16O) support piezometric evidence that groundwater primarily discharges to lakes but show further that mixing of groundwater and lake water has occurred at one site on Lake Victoria (Jinja). Layered-aquifer heterogeneity, wherein fluvial-lacustrine sands overlie saprolite, gives rise to both rapid and slow groundwater fluxes to lakes which is evident from the recession of borehole hydrographs following recharge events. Darcy throughflow calculations suggest that direct contributions from groundwater to Lake Victoria comprise <1% of the total inflows to the lake. Groundwater/surface-water interactions are strongly influenced by changing drainage base (lake) levels that are controlled, in part, by regional climate variability and dam releases from Lake Victoria (Jinja).