This study evaluated the impact of climate change on water resources in a large semi-arid urban watershed located in Niamey Republic of Niger, West Africa. The watershed was modeled using the fully integrated surface-subsurface HydroGeoSpheremodel at a high spatial resolution. Historical (1980-2005) and projected (2020-2050) climate scenario derived from the outputs of three Regional Climate Models (RCM) under the RCP 4.5 scenario were statistically downscaled using the multiscale quantile mapping bias correction method. Results show that the bias correction method is optimum at daily and monthly scales, and increased RCM resolution does not improve the performance of the model. The three RCMs predict increases of up to 1.6% in annual rainfall and of 1.58°C for mean annual temperatures between the historical and projected periods. The durations of the Minimum Environmental Flow (MEF) conditions, required to supply drinking and agriculture water, were found to be sensitive to changes in runoff resulting from climate change. MEF occurrences and durations are likely to be greater for (2020-2030), and then they will be reduced for (2030-2050). All three RCMs consistently project a rise in groundwater table of more than 10 meters in topographically high zones where the groundwater table is deep and an increase of 2 meters in the shallow groundwater table.