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Understanding the spatiotemporal distribution of future droughts is essential for effective water resource management, especially in the Mediterranean region where water resources are expected to be scarcer in the future. In this study, we combined meteorological and hydrological drought indices with the Soil and Water Assessment Tool (SWAT) model to predict future dry years during two periods (2035–2050and 2085–2100) in a typical Mediterranean watershed in Northern Morocco, namely, Bouregreg watershed. The developed methodology was then used to evaluate drought impact on annual water yields and to identify the most vulnerable sub-basins within the study watershed. Two emission scenarios (RCP4.5 and RCP8.5) of a downscaled global circulation model were used to force the calibrated SWAT model. Results indicated that Bouregreg watershed will experience several dry years with higher frequency especially at the end of current century. Significant decreases of annual water yields were simulated during dry years, ranging from −45.6% to −76.7% under RCP4.5, and from −66.7% to −95.6% under RCP8.5, compared to baseline. Overall, hydrologic systems in sub-basins under the ocean or high-altitude influence appear to be more resilient to drought. The combination of drought indices and the semi-distributed model offer a comprehensive tool to understand potential future droughts in Bouregreg watershed.