A better understanding of headwater hydrogeology in the semi-arid Andes is critical because high-elevation basins are considered water towers for the main valleys, where there is over-allocated water demand. While international literature generally focuses on the glacier contribution to streamflow, there is little information on the contribution of sparsely glacierized basins and the origins and processes of groundwater generation at high elevations. The Corrales catchment in North-Central Chile contains both glacierized and s parsely sub-basins as well as the highest public borehole in the region, making it suitable to fill such scientific gaps. Geophysical surveys and a pumping test were carried out to obtain information on groundwater flows beneath the Tapado terminal rock glacier and a main tributary of the Elqui river. Radioactive and stable isotopes were used to characterize the hydrological connectivity and the water origins of the headwater basins. Low electromagnetic velocities and resistivities reveal the presence of liquid water beneath the rock glacier, which could be the upper limit of a proglacial aquifer. The downstream valley aquifer appears transmissive and dominated by old waters (several decades) that are a mix of high-glacierized and low-glacierized basins. Additionally, stable isotopes indicate different signatures for high- and low-glacierized basins, which could result from isotope fractionation. These results indicate that water isotopes could be used to discriminate waters originating from high-glacierized and low-glacierized basins. The study identifies also the presence of old waters in the low-glacierized basins, which indicates long term storage, slow release or low turnover times. This finding is important for understanding late season baseflow and streamflow evolution in the context of climate change. As the contribution of such basins to total streamflow is significant, a better understanding of hydrological processes in sparsely glacierized regions is required.