Summary Three Global Climate Models (GCMs) output (precipitation and temperature), bias corrected with the WATCH Forcing Data (WFD), for the A2 and B1 scenarios, are used for drought assessment at a basin scale. At a first step, the hydrological model IHMS-HBV was calibrated using both local and large scale forcing data (precipitation and temperature) aiming to assess the suitability of large scale forcing data in a small basin, Platis, located in Crete, for the period 1974–1999. The second step includes the forcing of the WFD calibrated HBV model with the bias corrected GCM output from 2001 to 2100 (WATCH Driving Data). The produced hydrological variables, flow, soil moisture and lower groundwater reservoir volume were used for the hydrological regime assessment and drought identification with the aid of the threshold level method. A quantitative comparison with four future sub-periods was carried out addressing the drought events number, duration and deficit volume. Simulations of both emission scenarios indicate a significant decrease in all hydrological parameters. The relative change of drought characteristics for the future periods in terms of the three-model ensemble implied severe drought conditions. For A2 scenario, it was found that the number of drought events could increase up to 98%, 109% and 81% in flow, soil moisture and groundwater respectively. B1 scenario provided more conservative estimates, with an increase of drought events number up to 56%, 92% and 34% in flow, soil moisture and groundwater, respectively. The drought duration difference between scenarios reaches up to 33%, 89% and 34% for simulated flow, soil moisture and groundwater respectively till 2100. Moderate changes can be noticed in drought deficit volume with an estimated maximum increase of 19%, 33% and 22% in flow, soil moisture and groundwater involving A2 scenario, whereas B1 scenario projected 10%, 2% and 26% maximum increase for the former parameters. The evolution of the hydrological parameters is in line with the projected decreasing precipitation and increasing temperature trends.