Accurate and spatially distributed rainfall data are crucial for a realistic simulation of the hydrological processes in a watershed. However, limited availability of observed hydro-meteorological data often challenges the rainfall–runoff modelling efforts. The main goal of this study is to evaluate the Climate Forecast System Reanalysis (CFSR) and Water and Global Change (WATCH) rainfall by comparing them with gauge observations for different rainfall regimes in the Mara Basin (Kenya/Tanzania). Additionally, the skill of these rainfall datasets to simulate the observed streamflow is assessed using the Soil and Water Assessment Tool (SWAT). The daily CFSR and WATCH rainfall show a poor performance (up to 52% bias and less than 0.3 correlation) when compared with gauge rainfall at grid and basin scale, regardless of the rainfall regime. However, the correlations for both CFSR and WATCH substantially improve at monthly scale. The 95% prediction uncertainty (95PPU) of the simulated daily streamflow, as forced by CFSR and WATCH rainfall, bracketed more than 60% of the observed streamflows. We however note high uncertainty for the high flow regime. Yet, the monthly and annual aggregated CFSR and WATCH rainfall can be a useful surrogate for gauge rainfall data for hydrologic application in the study area.