The ecological state of the Inari Lake–Pasvik River system, the largest in northern Fennoscandia (in the near-border territories of Russia, Norway, and Finland) was assessed based on studying concentrations of heavy metals (HM) in the bottom sediments (BS). The water body (Kuetsjarvi Lake) contaminated with liquid wastes from the Pechenganickel smelter contains the highest HM (Ni, Cu, Co, Zn, Pb, Cd, Hg, and As) concentrations in the uppermost BS layers. In water bodies down and up the Pasvik River of the discharge site of waste waters from the smelter, the uppermost BS layers do not contain elevated concentrations of contaminating HM typical of the area (Ni, Cu, Co, Zn) but do contain higher concentrations of chalcophile elements (Pb, Cd, Hg, and As), which come mostly from trans-border sources. In the lakes receiving domestic wastes, phosphorus concentrations increase up the vertical section of the BS, which may suggest the development of eutrophication processes. They result in reducing conditions in the bottom waters and uppermost BS layers and, consequently, the transfer of ionic species of elements susceptible to variations in the redox potential from BS to waters. This process leads to depletion of the uppermost BS layers, first of all, in Fe and Mn and also in HM adsorbed on the surface of Fe and Mn oxides and hydroxides. In the water bodies that have preserved their oligotrophic nature, the uppermost BS layers were determined to accumulate Fe and Mn, whose concentrations are up to 50 times higher than the Earth’s crust average and the background values. Quantitative parameters of the factors and degrees of contamination are determined, as also are the ecological risk indexes for the contamination of the water bodies with HM, using the L. Hakanson method adapted to the regional conditions. The nonessential metals Hg and Cd, which are the most toxic and dangerous for hydrobionts, are determined to be the most ecologically hazardous in all of the water bodies. Nickel is a highly ecologically hazardous element in a single water body: Kuetsjarvi Lake. In all other water bodies of the Inari Lake–Pasvik River system, elements emitted and discharged by the smelter (Ni, Cu, Co, Pb, and As) are moderately and low ecologically hazardous for the aquatic systems.