This study aimed to quantify the effect of climate change on water balance and groundwater flow systems over the Walga-Darge watersheds. In this paper, Water and Energy Transfer between Soil, Plants, and Atmosphere under quasi-Steady State and MODFLOW were used to assess the hydrological impact of climate change. The Mann-Kendall test and Sen's slope estimator were used to analyze climate change. The mean annual temperature shows increasing trends, whereas the mean annual precipitation indicates decreasing trends. The simulated annual mean surface runoff is projected to decrease by 17.18, 22.04, and 31.37 for 2040, 2060, and 2080, respectively, compared to the 1980s. The model also indicates a reduction in precipitation and increased temperature causes a relative change in recharge, ranging from a decrease of 2.65, 38.82, 50.91, 61.57, and 75.49 in the 2000s, 2010s, 2040s, 2060s, and 2080s, respectively. The MODFLOW outputs furthermore show that annual groundwater discharge to the stream has decreased by -26.46% from 1985 to 2020 and is expected to decrease by -34.02% by 2080 due to climate change. The results of the study indicate that the increasing trends in temperature and decreasing rainfall amounts pose a significant threat to the sustainable use of water resources. HIGHLIGHTS center dot Temporal variation of climate data studied using the MK test and Sen's slope estimator center dot The impact of temporal variation in climate on hydrological balance and groundwater flow systems was studied using WetSpass and a three-dimensional groundwater model, MODFLOW. center dot The study shows that the increasing temperature and decreasing rainfall amounts pose a significant threat to hydrological balance and groundwater systems.