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Despite the general awareness that in Africa many people and large areas are suffering from insufficient water supply, spatially and temporally detailed information on freshwater availability and water scarcity is so far rather limited. By applying a semidistributed hydrological model SWAT (Soil and Water Assessment Tool), the freshwater components blue water flow (i.e., water yield plus deep aquifer recharge), green water flow (i.e., actual evapotranspiration), and green water storage (i.e., soil water) were estimated at a subbasin level with monthly resolution for the whole of Africa. Using the program SUFI‐2 (Sequential Uncertainty Fitting Algorithm), the model was calibrated and validated at 207 discharge stations, and prediction uncertainties were quantified. The presented model and its results could be used in various advanced studies on climate change, water and food security, and virtual water trade, among others. The model results are generally good albeit with large prediction uncertainties in some cases. These uncertainties, however, disclose the actual knowledge about the modeled processes. The effect of considering these model‐based uncertainties in advanced studies is shown for the computation of water scarcity indicators.