A multi-model hydrological assessment in the Congo Basin is performed to assess water availability conditions for historical and future periods (1913–2099). With models limited by scarce in situ observations, a combination of GRACE satellite data and soil-moisture-based drought indices is shown to be capable of estimating water budget, streamflow, and drought and storage variability. Changes in land use and land cover played a role in modifying the hydrologic responses but were found to be within the uncertainties of other inputs, including weather, soil, and model parameters. Seasonal and annual variability in total water storage anomalies (TWSAs) and the modified Palmer drought severity index (MPDSI) display a good correlation with each other. A selected set of global climate models is used to characterize the future temperature and precipitation patterns. It is expected that subbasin-scale variability in future temperature and precipitation increases will result in increased evapotranspiration, decreased runoff, and more drought events in the Congo Basin.