The study of water balance is considered here as a way to assess the performance of regional climate models and examine model uncertainty and as an approach to understanding regional hydrology, especially interactions between atmospheric and hydrological processes. We studied the atmospheric and terrestrial water balance over the Eastern Nile Basin (ENB) region using the weather research and forecasting (WRF) model. The model performance in simulating precipitation and surface air temperature is assessed by comparing the model output with the data from the Global Precipitation Climatology Center dataset for precipitation and from the University of Delaware for temperature. The results show that the simulated and observed values correlate well. In terms of water balance, the study region was found to be a sink for moisture, where the atmospheric convergence is negative during most of the time. Most of the precipitation originates from moisture fluxes from outside the domain, and the contribution of local evapotranspiration to precipitation is limited, with small values for the moisture recycling ratios year-round. The atmospheric moisture content does not show significant monthly or annual variation. The results indicate that the terrestrial water storage varies seasonally, with negative fluxes during most of the year, except June, July, and August, when most of the precipitation occurs.