Groundwater in high-mountain areas like the Central Chilean Andes is a crucial freshwater source for downstream communities. However, its pristine reputation masks a hidden threat when metallogenic systems exist: Natural Acid Drainage (NAD). This study comprehensively investigates the hydrogeological systems and the impact of NAD on groundwater quality in this copper-rich high-altitude region from an interdisciplinary approach. Specifically, the study area lies in the El Arpa Valley, a site with minimal human influence. Isotopic and hydrogeochemical analyses of groundwater, surface water, and snow samples revealed a groundwater origin between 2900 and 3300 m a.s.l. and the influence of fractures and gullies on recharge mechanisms. Physicochemical parameters exhibit increasing mineralisation downstream (118 to 714 mu S/cm) with a pH range of 3.86-7.01. SO42--Ca2+ facies and elevated aluminium (4.59-6349.31 ppb), iron (1.00-7003.24 ppb), and manganese (1.25-1098.41 ppb) contents characterise groundwater composition. Rock geochemistry and mineralogy show that phyllic alteration overprinted by supergene processes contributes to NAD by dissolving pyrite and iron oxyhydroxides. Principal component analysis on Landsat 8 images allows for identifying potential NAD areas over 11.6 % of the high Andes. The widespread occurrence challenges the perception of pristine mountain water, emphasising the potential adverse effects on human health and infrastructure, mainly due to high manganese content (>80 ppb). Findings advance the knowledge on NAD occurrence in remote mountainous regions, urging a reassessment of water quality perceptions in the presence of geogenic pollution sources, particularly considering the current threat of climate change.