In East Africa, climate change and variability have shown a strong impact on sectors such as agriculture, energy, and water. To allow mitigation and adaptation of the possible impacts of the projected change in climate, this study applies a Statistical Downscaling Model (SDSM) to generate a high-resolution climate projection, equivalent to future station data, to drive impact assessment models in selected, agricultural intensive, basins of Ethiopia (EthShed), Kenya (KenShed), and Tanzania (TanShed). Observed and large-scale climate variables (predictors) are obtained from the national meteorological agency of Ethiopia and international databases. BROOK90, a physical-based hydrological model, is used to assess the impacts of the projected change in precipitation and maximum and minimum temperature (T-max, and T-min) on the water balance. Based on SDSM, the results show an increase in precipitation, relative to the baseline period (1961–1990), in EthShed (14% - 50%) and KenShed (15% - 86%) and a decrease in TanShed (1.3% - 6.3%) in the 20s (2011–2040), 50s (2041–2070), and 80s (2071–2100) under the three Representative Concentration Pathways (RCPs; RCP2.6, RCP4.5, and RCP8.5). T-max (anomalies up to 3.7 °C) and T-min (anomalies up to 2.76 °C) will be warmer than the baseline period throughout the 21 century in all three basins. In line with the projected change in precipitation and temperature, an increase (decrease) in seasonal and annual streamflow, soil-water, and evaporation in EthShed and KenShed (TanShed) is projected in the 20s, 50s, and 80s. In general, sustainable adaptation measures are required to be developed in a site-specific manner, considering the projected increase in temperature and evaporation in all three basins and a decrease in soil-water and streamflow in TanShed.