Chemical pollution is a problem of global importance. Substances of main concern of chemists worldwide are heavy metals. Heavy metals, such as copper (Cu), nickel (Ni), lead (Pb), vanadium (V), etc., can pose a serious hazard to the environment and human health. Heavy metals are toxic even at very low concentrations. The methodology, described in this paper, considers a migration of chemical pollutants in the environment, in conjunction with the approach used in the Russian regulatory system. Estimations of Maximum Available Concentration overrun show that calculated and experimental data agree to a good extent, particularly for mercury contamination in freshwater bodies. In this study, due to the necessity to obtain data on heavy metals content in water, soil and air, based on available data on emissions, it was decided to use the USEtox model for the simulation of the redistribution of chemicals among such environmental compartments as urban air and air of settlements, fresh waters and coastal sea waters, ocean, agricultural soils and other soils. The USEtox model was chosen because it is available in the free access and its structure can be modified if needed (the model is executed in MS Excel), in addition there is a positive experience in using this model in the combination with Geographic Information Systems (GIS). The algorithm of the calculation of the mass transfer coefficients of chemicals in the hydrosphere and atmosphere, with the use of GIS, is described. This algorithm will provide large amounts of data on the intermedia transfer and transportation of chemical substances with water and air flows and their accumulation in various environmental compartments on a global (the planet Earth) and regional scale for the high-resolution of 0.5°×0.5° grid. In this paper, the case study for the Leningrad Region (the Russian Federation) is presented.