Due to the rapid socio-economic development in the Ethiopian Rift Valley basin, the pressures on water resources are increasing. To understand the change of spatio-temporal water fluxes, the hydrologic model SWAT+ (Soil and Water Assessment Tool+) was applied to five selected watersheds within the basin. With regards to the objective functions, Kling-Gupta efficiency (KGE: 0.68-0.84), the Nash-Sutcliffe efficiency (NSE: 0.61-0.73), percent Bias (PBIAS: -3.4 to 1.4), and RMSE-observations standard deviation ratio (RSR: 0.52-0.69), the SWAT+ model performed very well for daily streamflow in all watersheds. The change in water balance components indicated a considerable spatial variation of water fluxes in the watersheds. Precipitation, ET, and infiltration have generally decreased; but surface runoff has increased in the interference period compared to the baseline period. The spatial distribution of rainfall (-40 to 10%), evapotranspiration (-20 to 5%), surface runoff (7.8-13.1%), lateral flow (4.47 to -16.5%), and percolation (-3.3 to -10.2%) varied. The changes in the hydrologic system within the basin are greatly attributed to the combination of LULC change due to rapid population growth and climate variability.