The water table in southwestern Niger has been rising continuously for the past decades (4 m rise from 1963 to 2007), despite a ∼23% deficit in monsoonal rainfall from 1970 to 1998. This paradoxical phenomenon has been linked with a change in land use from natural savannah to millet crops that have expanded in area sixfold since 1950 and have caused soil crusting on slopes that has, in turn, enhanced Hortonian runoff. Runoff concentrates in closed ponds and then recharges the aquifer; therefore, higher runoff increases aquifer recharge. At the local scale (2 km2), a physically based, distributed hydrological model showed that land clearing increased runoff threefold, whereas the rainfall deficit decreased runoff by a factor of 2. At a larger scale (500 km2, 1950–1992 period), historical aerial photographs showed a 2.5-fold increase in the density of gullies, in response to an 80% decrease in perennial vegetation. At the scale of the entire study area (5000 km2), analytical modeling of groundwater radioisotope data (3H and 14C) showed that the recharge rate prior to land clearing (1950s) was about 2 mm a−1; postclearing recharge, estimated from groundwater level fluctuations and constrained by subsurface geophysical surveys, was estimated to be 25 ± 7 mm a−1. This order of magnitude increase in groundwater fluxes has also impacted groundwater quality near ponds, as shown by a rising trend in groundwater nitrate concentrations of natural origin (75% of δ15N values in the range +4 to +8‰). In this well-documented region of semiarid Africa, the indirect impacts of land use change on water quantity and quality are much greater than the direct influence of climate variability.