Understanding aquifer storage characteristics is critical for revealing river-aquifer interactions and is thus essential for effective water resource management. Hydrological studies often analyse watersheds as single units, potentially overlooking spatial variability in groundwater storage, especially in diverse hydrogeological settings. This study examines groundwater storage dynamics and river-aquifer interactions in the Chemoga watershed, Ethiopia, using a nested-watershed approach. Groundwater level data from eight monitoring stations and streamflow data from five gauging stations were integrated to assess groundwater storage dynamics. The Wilcoxon test revealed significant spatial variations (p < 0.05) in median groundwater levels from 1.3 to 17 m, exhibiting temporal sensitivity with a coefficient of variation of 18%-55%. When analysed as a single unit, the watershed exhibited a mean annual storage of 191 mm year-1. However, the nested-watershed approach uncovered a wide range of mean annual storage values, from -302 to +1777 mm year-1. Negative storage changes were observed in highland sub-watersheds (GS1, GS2) and the Wuseta River sub-watershed (GS4), whereas positive changes occurred in the midland floodplain (GS3) and lowland valley (GS5). These findings indicate that the Chemoga River acts as a gaining stream in the highlands but transitions to a losing stream in the midland floodplain and lowland valley. Additionally, a 1-month lag in baseflow response and hydro-stratigraphic evidence suggest potential lateral flow from GS3 to GS4 sub-watershed. This study highlights the limitations of treating watersheds as single units and advocates for spatially explicit approaches to better understand groundwater storage dynamics and river-aquifer interactions in complex hydrogeological environments.