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Selenga River brings to the Lake Baikal about 50% of the total river run-off, so that environmental state of the Selenga aquatic systems is of a primary importance for the sustainable development of Baikal as the Natural Heritage object. To assess the present hydrological regime and environmental geochemical state of the Selenga River basin the complex expedition was carried out in 2011-2014. The study area included both Russian and Mongolian parts of the basin. A special attention was paid to the Selenga River delta and main hotspots, such as large industrial towns and mining areas. The main results of the research include the elaboration of a unified hydrological and geochemical scheme of formation and transformation of water and material flows within the Selenga River basin. We conducted a description and obtained interim results of the development of modeling the water balance and transport of pollutants in the river basin. The environmental geochemical research of the Selenga aquatic systems revealed main spatial features of distribution of heavy metals and other pollutants in water, suspended matter and bottom sediments. The transboundary transport of heavy metals and their accumulation in the Selenga delta were determined based on quantitative analysis of geochemical flows.