Climate change significantly increases the risk of water resources scarcity by disrupting the hydrological cycle. Alterations in key variables such as temperature and rainfall directly influence water stored within the unsaturated soil layer and evapotranspiration (green water), as well as both of surface runoff and groundwater recharge (blue water). Nevertheless, much of the existing research has predominantly concentrated on the impacts of climate change on runoff, often highlighting shifts in rainfall and temperature patterns under historical and future scenarios, while largely neglecting the role of green water in water resource evaluations. This study explores the spatiotemporal variations of climate-sensitive water balance components and their impacts on blue and green water under both current and future climate scenarios using the Soil and Water Assessment Tool Plus (SWAT+) model in the Meki River sub-basin, located within the Rift Valley Lakes Basin of Ethiopia. Sensitivity analysis and model calibration were performed by utilizing the SWAT Toolbox v0.76. The results project a substantial decline in blue water availability by the end of the twenty-first century, by 48.7% and 56% under RCP4.5 and RCP8.5 scenarios, respectively, while green water is expected to increase by 22.7% and 24.4% under the same conditions. These outcomes underscore the critical need to integrate green water management into future water resource planning for the Meki River. Moreover, the methodological framework employed in this study presents a transferable approach that can be applied across the Ethiopian Rift Valley Lakes Basin and other regions experiencing similar hydrological challenges, providing a valuable basis for future investigations into blue and green water dynamics.