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| Uncertain climatic projections result in uncertain runoff predictions, which lead to unreliable water resources management and floods mitigation measures. This study investigates runoff uncertainty associated with Global Climate Models (GCMs) chosen as boundary conditions in regional climate models (RCMs). To this end, the study projected surface air temperature, precipitation, wind speed, and potential evapotranspiration, over Qatar, from the Massachusetts Institute of Technology (MIT) RCM driven by three GCMs: CCSM4, MPI-ESM, and NorESM. Historical projections were made during 1976–2005 while future projections were made during 2071–2100 under the business-as-usual Representative Concentration Pathways (RCP8.5). The study then inputs climatic parameters in addition to topographic and groundwater data, in a physically based water balance model to compare runoff simulations. During historical and future periods, climatic projections differed among the RCM runs, especially precipitation and potential evapotranspiration. Uncertainty in climatic projections caused significant uncertainty in runoff estimations. Runoff estimations varied from 12.2 to 45 Mm3 yr−1, with an average value of 24.4 Mm3 yr−1 during 1976–2005, and from 12.3 to 52.4 Mm3 yr−1, with an average value of 32.4 Mm3 yr−1 during 2071–2100. All RCM runs agreed on future runoff increases. Since runoff is a main cause of floods and alleviating flood risk can be hindered if climatic projections are incompetent, the study's findings emphasize on narrowing the uncertainty in GCM projections. The study also encourages Qatar authorities to implement managed aquifer recharge projects like rainwater harvesting to alleviate floods risk |