Climate change (CC) is likely to have a negative effect on water balance components thereby increasing global water scarcity. These effects, particularly in arid and semi-arid areas, have not been fully understood, in part because green water was not adequately represented in the relevant assessments. This study analyzes the spatiotemporal variations of blue and green water resources under baseline and future climate conditions by applying the Soil and Water Assessment Tool plus (SWAT+) model to the Meki River, located in Central Rift Valley (CRV) Lake Basins of Ethiopia. Based on sensitive parameters, identified from sensitivity analysis, we calibrated and validated the SWAT + model for the period from 1993 to 2000 and 1987 to 1992, respectively. During both the calibration and validation period, the model showed reasonable performance with a Nash-Sutcliffe efficiency of greater than 0.65. The model was then used to assess the effects of CC (representative concentrations pathways, RCP, 4.5 and 8.5) on the blue and green water components of the Meki River. We found that blue water is expected to decrease under both RCPs (4.5 and 8.5) scenarios, but anticipated to show a more decline of up to 56% under the RCP 8.5 scenario. Oppositely, green water is expected to increase under both scenarios, but RCP8.5 is projected to cause a larger increase (24%) when compared to the baseline. Overall, the integrated blue and green water modeling and assessment can be used as a tool to develop efficient strategies for water resources management of the Meki River.