In high mountain hydrosystems, glacial meltwater composition is potentially affected by the degradation of alpine permafrost terrains and ground ice bodies releasing atmospheric pollutants that have been stored in permafrost terrains for several decades. In this study we investigate the potential local permafrost distribution as well as the physical and chemical ground water characteristics of the periglacial environments of the Lago Nero (“Black Lake”) catchment, a high alpine basin located in the Southern Swiss Alps. Our approach combines in situ geological and geomorphological mapping, potential permafrost distribution modelling, a thermal monitoring of ground surface temperatures and the study of the meltwater chemistry of an intact rock glacier (active or inactive rock glacier, i.e. containing ice) and several perennial ice patches. The comparison of elemental concentrations between the periglacial terrains and the Lago Nero outflow unveiled the presence of atmospheric chemicals in the meltwater. Considering the temporal concordance between the recorded peak of sulphur deposition between 1965 and 1980 and the last identified period of positive glacier mass balance occurred in the region (1961–1985), we argue that the enhanced melting of ground ice related to the recent severe warming is nowadays releasing “legacy” pollutants that have been stored in the cryosphere for several decades.