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Mercury stress on the environment is one of the global challenges of our time. As a result of observations, it was discovered that the large rivers of Eurasia can be a source of transport of significant amounts of mercury to the Arctic Ocean [1]. Mercury and its compounds migrate between environmental components, contaminating water bodies. It poses a danger in aquifer systems: by the action of microbes the inorganic mercury converts to its highly toxic forms such as methyl- and dimethylmercury, minor exposures of which have devastating effects on central nervous system. Mercury in mercury-containing waste is prone to leaching, that causes its migration into aquifer systems. According to the research conducted in the Russian Federation, overall, in the course of production and use of mercury-containing consumer goods, 49.7 tons of mercury were released into the environment, or 3% of total mercury releases in 2012 [2]. We implemented in practice to assess the impact on the environment of mercury and its compounds entering from various anthropogenic sources with methodology for the integrated analysis of the global chemical load and using the concept of a chemical footprint. Additionally, an algorithm to evaluate the movement of chemicals with water masses with the use of GIS on a grid with a size of 0.5 to 0.50º has been developed. In this research work, estimates for the migration of Hg0, Hg2+ and such insoluble compounds as HgS were carried out separately. The obtained data on the content of mercury for environmental medias (e.g. freshwater) were summarized. In the figure you can see that for some regions of the Russian Federation the mercury footprint for freshwater body is greater than 1. This indicates a high risk of adverse environmental effects. As result we evaluated how immobilization of mercury in waste to the sulfide form may affect the volume of its entry into water bodies and on level mercury footprint. The reported study was funded by RFBR according to the research project № 18-29-24212.