The aim of this study is to examine the impact of climate change on runoff and potential evapotranspiration (PET) of Wadi Aqul, Saudi Arabia, using the Soil and Water Assessment Tool (SWAT). A novel farmwork was developed to generate hydrological multi-model ensemble from multiple General Circulation Models (GCMs) with the integration of hydrological model (SWAT). The performance of SWAT was promising on both daily and monthly scales (r(calib) > 0.85, r(valid) > 0.75). Climate change impacts were assessed over baseline (1979-2010) and future periods (near future, Q1: 2026-2050, mid future, Q2: 2051-2075, and far future, Q3: 2076-2100). The baseline period indicated a slight, non-significant decline in runoff, while future projections revealed variation: under moderate emission (SSP4.5), runoff decreased slightly in Q1 and Q2 but increased by 60% in Q3. Conversely, the high emission (SSP8.5) scenario showed consistent runoff increase across all quarters (Q1 = 15.9%, Q2 = 13.6%, and Q3 = 48.8%). The Modified Men-Kendell (mMK) trend analysis indicated significant positive trends under SSP8.5, especially in Q3 (Zc = 5.6, Tau = 0.30). Similarly, PET have showed rise under both scenarios, with SSP8.5 exhibiting higher increases (14.5-22.5% across Q1 and Q2) compared to SSP4.5 (7.6-10.6%). Trend analysis of PET revealed significant increases (p < 0.05), with the highest rise under SSP4.5 in Q2 (Zc = 5.53) and under SSP8.5 in Q3 (Zc = 8.14). The Box and whisker plots indicated high variability for runoff and PET under SSP8.5 than baseline and SSP4.5. These results highlight that SSP8.5 will lead to extreme hydrological conditions, underscoring the need for advanced water management strategies. Future research should incorporate high-resolution climate models and a multi-disciplinary approach to address the complex challenges of water resources in arid regions.