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Mediterranean region is identified as a primary hot-spot for climate change due to the expected temperature and rainfall changes. Understanding the potential impacts of climate change on the hydrology in these regions is an important task to develop long-term water management strategies. The aim of this study was to quantify the potential impacts of the climate changes on local hydrological quantities at the Goksu Watershed at the Eastern Mediterranean, Turkey as a case study. A set of Representative Concentration Pathways (RCP) scenarios were used as drivers for the conceptual hydrological model J2000 to investigate how the hydrological system and the underlying processes would respond to projected future climate conditions. The model was implemented to simulate daily hydrological quantities including runoff generation, Actual Evapotranspiration (AET) and soil-water balance for present (2005-2015) and future (up to 2100). The results indicated an increase of both precipitation and runoff throughout the region from January to March. The region showed a strong seasonally dependent runoff regime with higher flows during winter and spring and lower flows in summer and fall. The study provides a comparative methodology to include meteorological-hydrological modelling integration that can be feasible to assess the climate change impacts in mountainous regions.