Sustainable management of groundwater resources highly relies on the accurate estimation of recharge. However, accurate recharge estimation is a challenge, especially in data-scarce regions, as the existing models are data-intensive and require extensive parameterization. This study developed a process-based hydrologic model combining local and remotely sensed data for characterizing recharge in data-limited regions using a Basin Characterization Model (BCM). This study was conducted in Raya and Kobo Valleys, a semi-arid region in Northern Ethiopia, considering both the structural basin and the surrounding mountainous recharge areas. Climatic Research Unit monthly datasets for 1991 to 2020 and WaPOR actual evapotranspiration data were used. The model results show that the average annual recharge and surface runoff from 1991 to 2020 were 73 mm and 167 mm, respectively, with a substantial portion contributed along the front of the mountainous parts of the study area. The mountainous recharge occurred along and above the valleys as mountain-block and mountain-front recharge. The long-term estimates of the monthly recharge time series indicated that the water balance components follow the temporal pattern of rainfall amount. However, the relation of recharge to precipitation was nonlinearly related, showing the episodic nature of recharge in semi-arid regions. This study informed the spatial and temporal distribution of recharge and runoff hydrologic variables at fine spatial scales for each grid cell, allowing results to be summarized for various planning units, including farmlands. One third of the precipitation in the drainage basin becomes recharge and runoff, while the remaining is lost through evapotranspiration. The current study’s findings are vital for developing plans for sustainable management of water resources in semi-arid regions. Also, monthly groundwater withdrawals for agriculture should be regulated in relation to spatial and temporal recharge patterns. We conclude that combining scarce local data with global datasets and tools is a useful approach for estimating recharge to manage groundwater resources in data-scarce regions.