The study of subsurface water in the high-carbon (shungite-bearing) rock area of the Onega structure and laboratory experiments on interactions between the rock and water showed that sulfides widely present in high-carbon rocks are the cause of the formation of sulfate-type waters. Oxic conditions initiate the oxidation of sulfides and the formation of soluble sulfates. Depending on the stage of the process, the mineral composition of the host rock and the migration conditions, the subsurface water, being predominantly of the sulfate type, acquires different pH values and a varying composition and spectrum of trace elements. Acid effluents formed during the open mining of shungite-bearing rock can have negative environmental consequences. In some cases, the concentrations of sulfates, iron and other ore elements limit the usability of the water for drinking purposes, but sometimes they form mineral healing water. This type of water is most likely associated with the dissolution of sulfide oxidation products accumulated during the Late Weichselian glaciation, followed by neutralization of acidity due to interaction with the host rock.