<p>In the main Ethiopian rift, litho-structural complexity and scant study on factors that control water well productivity pose difficulty in predicting well yield. This study examines the relationship between well yield and geological structures in the Gidabo watershed, southern main Ethiopian rift valley, through the characterization of physical hydrogeology. Litho-structural data was compiled from the existing maps and remotely sensed data. Lithologic log and well yield data were compiled from water well drilling completion reports. Fieldwork was conducted for data verification. Well yield data were plotted on the ArcGIS environment, and a cross-section was constructed to conceptualize well yield spatial variation and its relation to faults. The study reveals that well yield varies between 1.5 and 184 lit/sec with no systematic spatial distribution and statistically significant relation to surface elevation as well as well depth. The high-yield wells (&gt; 8 lit/sec) are encountered along the long E-W trending fracture lines, and the low-yield wells (&lt; 8 lit/sec) are either associated with the short lineament or the Wonji faults that are not connected to the long E-W trending lineaments. Further, wells drilled on the dip side of the first-encountered east-dipping Wonji fault along flow lines are marked by high yield. In contrast, wells drilled on the opposite side of the east-dipping first-encountered fault or beyond towards the west have low yield unless drilled along the long E-W trending lineaments. This finding guides groundwater development activities in the Gidabo watershed and in the hydrogeologically similar Ethiopian Rift Valley.</p>