The article presents the first data on the study of a wide range of chemical elements in the water and sediments of small lakes located in the Arctic Zone of Russia. Among the selected objects are two lakes located in the urbanized areas. As a result, the sediments of all lakes were classified by the ratio of the main elements and the total content of organic matter. The concentration coefficients of all elements were calculated taking into average concentrations of different elements in the continental crust and the potentially toxic elements in the sediments of the background area. Analyzing sediment cores made it possible to evaluate the historical dynamics of the behavior of some metals and metalloids (Pb, Cd, Sb, Sn, Bi, Ni, Cu) in the aquatic environment during the industrial era, both in urbanized territories and in the background regions of the Arctic. The main natural and anthropogenic factors of the formation of geochemical anomalies in the concentrations of different elements, including potentially toxic ones, in the sediments studied, were identified. In urban areas, the main sources of metals entering the lake environment are emissions of the copper–nickel, thermal power plants, coal port, and an incineration plant. For all lakes, the pollution level of objects was estimated by calculating the geo-accumulation index and pollution load index. The most polluted lakes are the lakes of urban areas of the Arctic, the lakes of the background territories are characterized by a moderate level of pollution or no pollution.