Peter the Great Bay and Lake Khanka are among the most important structural and industrial fishing parts of the Far East coastal ecosystem, which are used by a number of countries such as Russia, China, Korea, Japan, etc. At the same time, the active use of water resources, as well as industrial activities deployed on the coastal part of these reservoirs, are accompanied by a constant flow of pollutants into the water area. Among them, one can include heavy metals; their entry and migration are currently not fully controlled. There exists an important scientific and ecological task to study the features of heavy metal migration and transformation in natural objects. Bottom sediments act as a substrate for hydrobionts and, at the same time, serve as accumulators of pollutants, so that they can be used as the main component of the coastal-shelf ecosystem. The geochemical assessment of the behavior of heavy metals in the bottom sediments of Ussuri Bay and Amur Bay (Sea of Japan) and Lake Khanka (Xingkai) has been performed. Qualitative and quantitative elemental compositions of the bottom sediments have been established by means of the inductively coupled plasma-mass spectrometry (ICP-MS), atomic absorption spectrometry (AAS), and X-ray fluorescence analysis (XRF), whereas a correlation with the concentration of elements in seawater above sediments has been provided. The main phases of anthropogenic components as well as their relationship with an increased content of heavy metals have been established using X-ray diffraction analysis (XRD). Average values of the concentration of elements in the bottom sediments of Peter the Great Bay decrease in the following row: Fe > Cu > Cr > Zn ≥ Pb > Mn > Ni, and for Lake Khanka: Pb > Cu > Mn > Fe > Cr > Zn > Ni. Here, the excessive contents of Cr, Fe, Cu, Zn, and Pb in sea bottom sediments by 6, 32, 7, 3, and 4 times as compared with background values are the result of the formation of a large amount of carbonate and iron-oxide phases. At the same time, it was shown that, during the transition from the estuarine (coastal) area of river flow to the central (closer to the outlet to the ocean), the concentration of biogenic metals (Ni, Zn, Pb, Cu) generally decreased 2–4-fold along the profile, which was associated with the formation of their hydroxides and carbonates in the area of mixing of freshwater and seawater followed by that of complex compounds or absorption. A significant anthropogenic impact is observed in the lake sediments, which is demonstrated by the excess of Pb concentration by 6700 times, as compared with the Clarke number of the lithosphere. The non-uniform distribution of heavy metals along the core profile has been established, which is related to different contents of aluminosilicate and iron oxide phases in the form of hematite and magnetite. The sedimentation rate has been established by means of granulometric and radiometric analysis and equaled to 0.45 mm/year in Ussuri Bay, 1.6 mm/year in Amur Bay, and 0.43–0.50 mm/year in Lake Khanka. By calculating the distribution coefficients of heavy metals in the ‘water–deposits’ system, some features of migration and accumulation of individual elements have been established. To assess the potential pollution of the marine areas, the geoaccumulation index (Igeo) and the pollution factor (Kc) have been calculated. In comparison with the maximum permissible concentrations of the Russian Federation (MPC), the World Health Organization (WHO), the US Environmental Protection Agency (US EPA), and environmental protection agencies of China and Japan, Peter the Great Bay has an excess of Mn—2-fold, Fe—2-fold, Zn—3-fold, whereas in Lake Khanka, the situation is even less favorable, in particular, the excess of Mn is 79-fold, Fe—35-fold, Cu—2-fold, Zn—3–4-fold, which is clearly determined by the closeness of the water basin and the lack of water exchange. In comparison with the lithosphere Clarke number, the sediments of both water basins, as well as the coastal soil of the lake, are enriched with Pb and depleted with Cr, Ni, and Zn. The highest values of Igeo in both water basins have been observed for Pb, and equaled 12–16 in Peter the Great Bay and 6000 in Khanka Lake. Based on the data obtained, the areas with the greatest pollution caused by natural and anthropogenic factors have been identified. Full article