Estimating the spatial and temporal patterns of groundwater recharge through integrated water balance modeling plays an important role in sustainable groundwater resource management. Such modeling effort is particularly essential for data-scarce regions, such as the Rift Valley Lake basin in the Basement Complex of Ethiopia, which has shallow aquifers, a proliferation of wells, and poor groundwater monitoring networks. A spatially distributed water balance model (WetSpass), along with GIS and remote sensing tools, was used for groundwater recharge estimation for its suitability and efficiency in data-scarce hydrogeological regions. The WetSpass model depicted a very good performance in simulating the groundwater recharge in the Upper Gelana watershed within the Rift Valley Lake basin. The water balance analysis revealed that about 7% of the mean annual rainfall is converted to groundwater recharge, and the remaining rainfall amounts are partitioned into surface runoff (19%) and evapotranspiration (75%). The model simulation outputs are also used to investigate the relative influences of biophysical driving factors on the water balance components. While the land use types had a greater influence on the actual evapotranspiration processes, the soil texture classes were the dominant factors in the surface runoff and groundwater recharge processes in the watershed. The groundwater recharge rates were found to be higher than 400 mm/yr in the central parts (Fisehagenent, Tore, and Gedeb) and lower than 165 mm/yr in the southern parts (Hageremariam) of the watershed. The areal proportions of the low, medium, and high recharging parts of the watershed are, respectively, estimated as 15%, 68%, and 17% of the watershed area. Therefore, the spatial and temporal patterns of groundwater recharge should be taken into consideration in developing a sustainable groundwater resources management plan for the Upper Gelana watershed. Managed aquifer recharge can be adopted in high and medium groundwater recharging parts of the watershed to capture stormwater runoff during the wet season to improve the groundwater supply during dry months. Furthermore, monthly groundwater withdrawals should be regulated according to the spatial and temporal patterns of the groundwater recharge in the watershed.