The results of quantitative determination of 30 elements in surface waters, snowmelt and rainfall, and 49 elements in bottom silts of mountain lakes of the Iolgo Range (Altai Mountains) using inductively coupled plasma mass spectrometry (ICP-MS) were obtained. The physicochemical characteristics of water bodies (pH, oxidation-reduction potential (ORP), electrical conductivity) were studied. Surface waters are ultra-fresh (mineralization 5.7–43 mg/l), slightly alkaline to alkaline (pH – 7.6–9.0), ORP corresponds to the oxidizing geochemical environment (166–225 mV). In the cascade of Karakol lakes from the upper part of the valley downstream of the Tura River, the total mineralization of water decreases, and the pH changes from alkaline to slightly alkaline. The main factors in the formation of the most alkaline and mineralized waters of all those studied in the upper Karakol lakes are the geochemical features of the bottom silts of these lakes, as well as their stagnant nature, which contributes to the accumulation of elements over a long period of time. High solubility of carbonates in contact with low-mineralized melted snow water at low water and air temperatures in the area of the upper lakes also contributes to the formation of alkaline conditions in the water. The water of all the lakes belongs to the calcium group. The predominant elements in the snowfield are Na, K, Ca, in rainfall – K, Si, Ca. The content of pollutants does not exceed the MAC in drinking water. Lake silts inherit geochemical markers of the underlying volcanics, indicating the geodynamic setting of their formation. The element distribution trends in bottom silts normalized by the primitive mantle are characterized by enrichment in light lanthanides and LILE, depletion in heavy lanthanides, and pronounced minima in Nb, Ta, and Ti, which is an indicator of the presence of subduction-related rock weathering products in their composition (in the active continental margin zone). The study objects are located within the Sagany-Kylay lead-zinc ore region with Pb, Cu ore occurrences and W, Zn, and Be lithochemical anomalies. Increased content of these and associated metals is recorded both in the watercourses of the Tura and Ugul river basins and in the bottom silts of lakes. In surface waters, the contents of Ni, Zn, Pb exceed the clarke values, in lake silts – Be, Sc, V, Cu, Zn, Mo, Cs, Hf, W, Pb, which corresponds to the metallogenic specialization of this region.