Mountain ranges cover approximately 24% of the Earth's land mass. These environments have a special relevance in terms of global water supply. However, historically mountain groundwater processes have been generally overlooked or poorly understood, especially in the Andes cordillera. With this in mind, this work aimed to study hydrological processes in four Andean, semi-arid headwater river basins. Along with monthly stable isotope data collection, we carried out a synoptic surface water sampling programme in each river on four specific dates for 3H analysis. The latter indicated water of similar age in the rivers of three sub-basins (Derecho, Cochiguaz, Incaguaz), but much older in the fourth (Toro). We assessed different possible explanations for these differences such as effects of past mining activities (El Indio mine), physiographic factors and snow accumulation and glacier related factors, but none of these were satisfactory. Instead, our findings point to the activation of faults in response to seismic activity, which induces pumping of fluids (water) from deeper zones, facilitating exfiltration processes in the Toro River sub-basin. This explains the presence of surface waters older than those associated with current meteoric processes. Such geological process should be assessed and eventually accounted for when studying mountain hydrogeological processes, especially in high fractured areas with direct or indirect evidence of geothermal activity.