Mining regions in different parts of the world have been associated with the significant pollution of water, sediments, and soils by manganese and other chemical elements. This study assessed the degree of geochemical transformation caused by open-pit extraction and processing of mineral resources in the Kovdorsky District of Murmansk Oblast, 20 km from the Russia–Finland border. A second objective was to predict further changes co-driven by industrial pressure and high climatic instability in the polar region. The field study involved sampling water and sediments from virgin background streams and from the tailings storage facility, settling ponds, rivers, and lakes affected by ore mining and disintegration. Laboratory analyses included the study of elemental composition, redox potential, alkalinity and acidity, organic matter content, and other geochemical characteristics for a better understanding of pollutant migration patterns. We revealed elevated levels of potentially toxic elements in surface waters and bottom sediments which pose a risk to the human health via the household and drinking water supply. Pollution with manganese (Mn) was found to be the major environmental issue. Its natural presence in the river water was overridden a hundredfold by anthropogenic enrichment. This is problematic as Mn is easily bioaccumulated, which can lead to unwanted ecotoxicological effects, and—in the case of prolonged exposure to high doses of Mn and its compounds—to detrimental human health impacts. We believe that the changing climate may raise the water flow and thus expand the area of the hydrochemical anomaly. On the other hand, the activation of self-purification and dilution processes could lead to decreasing environmental Mn concentrations.