The utilization of groundwater has emerged as an indispensable asset in facilitating economic advancement, preserving ecological integrity, and responding to the challenges posed by climate change, especially in regions characterized by aridity and semi-aridity. The sustainable management of water resources requires an assessment of the geographical and temporal patterns of groundwater recharge. The present study employed the GIS-based WetSpass-M model to model the water balance components by utilizing hydro-meteorological and biophysical data from the Wabe catchment, which spans an area of 1840 km2 in central Ethiopia, for a long time. The objective of this study was to assess the long-term average annual and seasonal groundwater recharge for the catchment area utilizing the WetSpass-M model. The input data were collected through remote sensing data and surveys in the field. The model was employed to gain insights into the process of groundwater recharge in a particular region and to facilitate effective management, prudent utilization, and sustainable planning of water resources in the long run. Water balance components were estimated using seasonal fluctuations in evapotranspiration, surface runoff, and groundwater recharge. The Wabe catchment’s summer, winter, and mean long-term yearly groundwater recharge were determined to be 125.5 mm, 78.98 mm, and 204.51 mm, respectively. The model indicates that summer seasons account for 86.5% of the mean annual precipitation, while winter seasons account for 13.5%. On the other hand, the groundwater system percolates 14.8% of the total annual rainfall (1374.26 mm). While evapotranspiration accounts for 51% of total precipitation and surface runoff accounts for 34.1%, the Wabe catchment’s mean annual evapotranspiration and surface runoff values are simulated at 701.11 mm and 485.58 mm, respectively. The findings suggest the use of the WetSpass-M model to precisely calculate the water balance components within the Wabe catchment.