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The Selenga River flows from mountainous part of Mongolia into the Baikal Lake in Russia. The Selenga River Delta covers about 540 sq km and accumulates more than a half of suspended matter and pollutants that comes from the basin. The main sources of pollution in the basin are associated with urban and mining areas. In Mongolia there are Ulaanbaatar city, industrial towns of Erdenet and Darkhan, while in Russia Ulan-Ude town and W-Mo processing factory in Zakamensk. Boroo and Zaamar gold mining areas are the main mining activities and situated in Mongolian part of the basin. Among 71 elements 10 main pollutants was chosen. Within 10 heavy metals it was revealed that average content in water of V, Mn, Fe, Cu, Zn, Mo is above Maximum Permissible Concentrations for fishery waters. And content of Mn, Ni, As and U in the suspended matter is higher than average composition of upper continental crust according to K.H.Wedepohl. The aim of this study was to detect the levels of pollutants and their spatial distribution within the Selenga Delta area. Thus zones of different pollution levels was defined: maximum concentrations were found in eastern and western parts in channels with big discharges.