Little is known of the interactions between groundwater and surface water on the deeply weathered surfaces of low relief in the Great Lakes Region of Africa (GLRA). The role of groundwater in sustaining water levels in lakes, rivers and wetlands during periods of absent rainfall is also unclear. Indeed, groundwater is commonly excluded from estimations of the surface water balances. Piezometer nests constructed on the shores of Lakes Victoria (Jinja, Entebbe) and Kyoga (Bugondo) through this study, provide the first evidence of the lithologic interface and dynamic interactions between groundwater and surface water in the GLRA. Evidence is drawn from lithological analyses (texture, lithostratigraphy), geophysical surveys (resistivity mapping, VES), hydraulic tests, borehole hydrographs and hydrochemical (major ions, \delta^2H, \delta^1^8O) data. Groundwater interacts with surface waters primarily via preferential pathways within the coarse horizons towards the base of thick saprolite underlying relatively thin (<5 m) fluviallacustrine sands. Hydrological observations and hydrochemical data indicate that groundwater flows primarily into lakes; this interaction is dynamic varying by season and proximity to lake. Interactions between groundwater and Lakes Victoria and Kyoga are also influenced by changing drainage base (lake) levels that are controlled, in part, by regional, rather than local climatology and dam releases from Lake Victoria (Jinja). Groundwater levels are strongly influenced by rainfall-fed recharge that depend more upon heavy rainfall events (10 mm\cdot d^-^1) during the monsoons than the total volume of rainfall; mean vertical velocities in the unsaturated zone are ~1 m\cdot d^-^1. Layered heterogeneity in aquifer properties (hydraulic conductivity, storage) indicate deeply weathered rocks formed under prolonged in situ weathering (etchplanation) of lowrelief surfaces. This layered heterogeneity in the saprolite aquifer gives rise to a twocomponent recession in borehole hydrographs following recharge events. A firstapproximation of the proportion of the Lake Victoria’s water balance supplied by groundwater is derived from new observations in this study and is in the order of 1 %
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