In the 21st century, changes in induced climate can significantly affect the water resources system in the watershed. Understanding climate change disrupts hydrological processes can facilitate sustainable water resource strategies to resilient impacts of global warming. The hydrological response of watersheds will be accelerated by climate change, altering the rainfall, magnitude & timing of runoff, and sediment yield. The study investigates climate change aspects on the hydrological responses using Soil and Water Assessment Tool (SWAT) model interfaced with Geographical Information System (GIS) of Genale Basin, Ethiopia. The calibrated SWAT was applied to simulate the impact of climate, and the SUFI-II algorithm was used for parameter optimization & finalization. The change of climate scenarios was built using the outcomes bias-corrected CORDEX RCM daily precipitation, min/max temperature for Ethiopia under RCP 4.5 and RCP 8.5. The average monthly change of streamflow from −16.47% to 6.58% and − 3.6% to 8.27% under RCP4.5 and RCP8.5, respectively (2022–2080). The monthly average sediment yield change was −21.8% to 6.2% and − 5.6% to 4.66% for the RCP4.5 and RCP8.5 scenarios, respectively, over 2022–2080. It implies that the climate change-induced impacts on sediment yield are more significant than streamflow and suggest substantial adaptive management in watershed systems.