This study analyzes the impact of climate change on freshwater availability in Africa at the subbasin level for the period of 2020-2040. Future climate projections from five global circulation models (GCMs) under the four IPCC emission scenarios were fed into an existing SWAT hydrological model to project the impact on different components of water resources across the African continent. The GCMs have been downscaled based on observed data of Climate Research Unit to represent local climate conditions at 0.5° grid spatial resolution. The results show that for Africa as a whole, the mean total quantity of water resources is likely to increase. For individual subbasins and countries, variations are substantial. Although uncertainties are high in the simulated results, we found that in many regions/countries, most of the climate scenarios projected the same direction of changes in water resources, suggesting a relatively high confidence in the projections. The assessment of the number of dry days and the frequency of their occurrences suggests an increase in the drought events and their duration in the future. Overall, the dry regions have higher uncertainties than the wet regions in the projected impacts on water resources. This poses additional challenge to the agriculture in dry regions where water shortage is already severe while irrigation is expected to become more important to stabilize and increase food production.