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The Selenga River transboundary basin is located on the territory of Russia and Mongolia and is characterized by a complex geological structure, diversity of natural conditions, as well as sharply increasing anthropogenic influence, manifested, in particular, the contamination of terrestrial and aquatic ecosystems by heavy metals. The study aimed at identifying characteristics of migration and accumulation of heavy metals in aquatic systems, quantitative assessment of transboundary transport of heavy metals and their deposition in the Selenga delta. Analysis of the heavy metal levels in rivers of the Selenga basin showed that average content of Fe, Al, Mn, Zn, Cu, Mo, V in water is above MPC fishery values. Spatial analysis of distribution of heavy metals and other pollutants in water, suspended matter and bottom sediments revealed the mostly polluted areas of the basin. Main features of geochemical fluxes of dissolved and suspended forms of heavy metals were determined.