This paper aims to provide a procedure to improve the estimations of freshwater availability at the sub-basin level and monthly intervals. Applying the distributed hydrological model Soil and Water Assessment Tool (SWAT), the freshwater availability is quantified for a 4-million km2 area covering some 18 countries in West Africa. The procedure includes model calibration and validation based on measured river discharges, and quantification of the uncertainty in model outputs using the Sequential Uncertainty Fitting Algorithm.