This paper presents a methodology for hydrograph separation in mountain watersheds, which aims at identifying flow sources among ungauged headwater sub-catchments through a combination of observed streamflow and data on natural tracers including isotope and dissolved solids. Daily summer and bi-daily spring season water samples obtained at the outlet of the Juncal River Basin in the Andes of Central Chile were analysed for all major ions as well as stable water isotopes, δ18O and δD. Additionally, various samples from rain, snow, surface streams and exfiltrating subsurface water (springs) were sampled throughout the catchment. A principal component analysis was performed in order to address cross-correlation in the tracer dataset, reduce the dimensionality of the problem and uncover patterns of variability. Potential sources were identified in a two-component U-space that explains 94% of the observed tracer variability at the catchment outlet. Hydrograph separation was performed through an Informative-Bayesian model. Our results indicate that the Juncal Norte Glacier headwater sub-catchment contributed at least 50% of summer flows at the Juncal River Basin outlet during the 2011–2012 water year (a hydrologically dry period in the Region), even though it accounts for only 27% of the basin area. Our study confirms the value of combining solute and isotope information for estimating source contributions in complex hydrologic systems, and provides insights regarding experimental design in high-elevation semi-arid catchments. The findings of this study can be useful for evaluating modelling studies of the hydrological consequences of the rapid decrease in glacier cover observed in this region, by providing insights into the origin of river water in basins with little hydrometeorological information.