The Kara River watershed (KRW), northern Togo, is facing climate-change impacts that have never been clearly characterized. Six decades of rainfall data (1961–2020) from six measuring stations ideally distributed across the watershed were used in this study. The flow records from two stations situated in contrasting locations on the KRW were also used. Statistical tests were conducted to assess the spatial and temporal variability of the rainfall and to detect tendencies within these meteorological series. The water balance method and calculation of the dry-off coefficient and of the groundwater volume drained by rivers allowed evaluating the impact of climatic evolution on surface flow and on groundwater volumes during the six decades studied. The results showed contrasting spatiotemporal variability of rainfall (and of aquifer recharge) over the watershed with a decreasing tendency upstream and an increasing one downstream. At the same time, the water volume drained by the aquifer to sustain the river’s base flow decreased from −22% to −36% depending on the measuring station. These results constitute a decision-making tool for Togolese water resource managers and are of primary importance for characterizing the fate of water resources worldwide in regions subject to severe droughts.