This study investigates the impacts of climate change on the hydrological response of a Mediterranean mesoscale catchment using a hydrological model. The effect of climate change on the discharge of the Alata River Basin in Mersin province (Turkey) was assessed under the worst-case climate change scenario (i.e., RCP8.5), using the semi-distributed, process-based hydrological model Hydrological Predictions for the Environment (HYPE). First, the model was evaluated temporally and spatially and has been shown to reproduce the measured discharge consistently. Second, the discharge was predicted under climate projections in three distinct future periods (i.e., 2021–2040, 2046–2065 and 2081–2100, reflecting the beginning, middle and end of the century, respectively). Climate change projections showed that the annual mean temperature in the Alata River Basin rises for the beginning, middle and end of the century, with about 1.35, 2.13 and 4.11 °C, respectively. Besides, the highest discharge timing seems to occur one month earlier (February instead of March) compared to the baseline period (2000–2011) in the beginning and middle of the century. The results show a decrease in precipitation and an increase in temperature in all future projections, resulting in more snowmelt and higher discharge generation in the beginning and middle of the century scenarios. However, at the end of the century, the discharge significantly decreased due to increased evapotranspiration and reduced snow depth in the upstream area. The findings of this study can help develop efficient climate change adaptation options in the Levant’s coastal areas.