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Currently, water demands are in continuous growth which increases the pressure, in quantity and quality, on the water resources available over the world. Likewise, the projected reduction of natural water inputs, due to climate change, represents a new level of uncertainty. Despite existing errors, hydrological models are important tools for planning and managing water resources. Their correct application is essential in areas with high water stress (arid and semi-arid regions). The Segura River basin district (DHS), southeastern Spain, has one of the highest scarcity rates and intensive exploitation of water resources in Europe and the world. This study estimates the effects of climate change on the main components of the water balance in the upper basin of the Taibilla River (the headwater of the DHS). This basin has been chosen because it is in natural regime and it is currently one of the main water supplies in many DHS municipalities and contiguous areas. In order to assess the mentioned effects, we used the Soil and Water Assessment Tool (SWAT) calibrated with the SUFI-2 algorithm. Calibration and validation were performed with two objective functions (NSE and KGE) in the period with availability of discharge data (1996-2012). The precipitation and temperature projections came from the global climate models (GCMs) bcc-csm 1 - 1-m, MPI.ESM.MR and bcc.csm1.1, regionalized with the analogue technique, under the emission scenarios RCP4.5 and RCP8.5 (period 2010-2050). The adjustment results improved with NSE, with respect to KGE, in the calibration and validation series. In the future decades, precipitation, surface runoff and recharge of aquifers would show negative trends while the temperature would increase by between 1.5 degrees C and 1.7 degrees C. In spite of the existing uncertainty, it is evident that natural water inputs will decrease in this river basin. This will be a challenge in the water resources management for local authorities. The obtained results can assist local authorities at decision making regarding hydrological planning and the fight against climate change in the DHS. In addition, SWAT as a rainfall-runoff conversion tool, together with the implemented models and climate change scenarios, are suitable in an area with subhumid and semi-arid climate and can be used in other regions with similar climatology.