An extensive and year-round survey was conducted to assess metal pollution in vast watershed areas of the Selenga River Basin (2007-2009), which provided baseline heavy metal database for the future management. Sources and environmental hazard and risk indices associated with metal pollution were evidenced across the countries of Mongolia and Russia (Buryatia Republic). In general, the concentrations of heavy metals in river water of Mongolia were greater than those of Russia, expect for the upstream of the Dzhida River in Russia. The spatial distribution generally indicated that metal pollution in the Selenga River was mainly associated with the activities in the Mongolian upstream regions. Similar pollution sources of metals between river water and wastewater associated with surrounding activities were found across the industrial and mining areas. Compositional patterns of metals suggested their sources were independent of each other, with hot spots in certain sites. Our measurements indicated that about 63 % of the locations surveyed (48 of 76) exceeded the critical heavy metal pollution index of 100, identifying possible harmful effects on aquatic ecosystems through metal pollution. Zinc was found to be the chemical of priority concern, as more than half of the locations exceeded the corresponding water quality guideline. Other metals including Mn, Fe, Cr, Cu, and As might be problematic in the Selenga River Basin considering the occurrence and their concentrations. Results of our extensive survey during the period of 3 years indicated that urgent action would be necessary in timely manner to improve water quality and mitigate the impact of heavy metals on aquatic environment of the Selenga River Basin.