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 water demand is the highest. Geophysical surveys and a pumping test were carried out to obtain information on aquifer structures and properties. Radioactive and stable isotopes were used to characterize the hydrological functioning of the headwater basins. Low electromagnetic velocities and resistivities reveal the presence of liquid water beneath a rock glacier, which could be the upper limit of a proglacial aquifer. The downstream valley aquifer appears fairly transmissive (3.2 10 ^-3 m ²s ^-1) and dominated by old waters (several decades) that are a mix of high-glacierized and low-glacierized basins. Additionally, stable isotopes point out a different signature for high-glacierized 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 the presence of old waters in a priori low-glacierized basins, which indicates long term storage. 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, studies that aim to predict streamflow should not only focus on basins containing large glaciers.