Geba River Basin, which is the site of high socio-economic importance, is affected by high water stress, frequent drought, flooding, and soil erosion. Yet, its hydro-geomorphology is not well investigated. This study focuses on characterizing the hydro-geomorphology of sub-watersheds found in the Geba River basin in terms of their topographic ruggedness, groundwater recharge potentiality, and soil erosion susceptibility. During the study, many step-wise procedures have been followed: First, the entire drainage basin was segmented into 12- sub-watersheds using the DEM as a database and GIS as a data processing environment. Second, the drainage network of each of the watersheds was generated by assigning a common threshold value. Third, geomorphic parameters that characterize the sub-watersheds were quantified using the GIS processing function and standardized mathematical equations. Forth, the compound factor value of each of the parameters was calculated using the weighted sum approach. Finally, using the calculated compound factor as an input, the sub-watersheds were ranked in terms of their topographic ruggedness, groundwater recharge potentiality, and soil erosion susceptibility. Results show that sub-watershed-5, sub-watershed-8, and sub-watershed − 9 are characterized by a steep slope and high rugged topography compared to the other sub-watersheds. Further, sub-watershed-4 and sub-watershed-6 are the most promising sites for groundwater recharge potential. Moreover, sub-watershed-1, sub-watershed-5, and sub-watershed-9 are the most susceptible to soil erosion. It is strongly believed that the output of this work helps planners and decision-makers in resource conservation measures and selection of groundwater recharge potential sites.