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In recent years, increasing attention is drawn to the Lake Baikal water quality due to the growth of human activities in its catchment area. A special attention is paid to the transboundary Selenga River as a major tributary of Baikal experiencing growing impact from industrial towns and mining activities. Our research aims to assess quantitatively the geochemical fluxes of heavy metals both in dissolved and suspended forms in aquatic systems of the Selenga River and its tributaries. The study is based on about 200 samples of river water and suspended matter collected during the high water period in August 2011 and the low water period in June 2012. The contents of heavy metals were obtained by ICP-MS and ICP-AES methods. The study revealed the significant increase of the heavy metal fluxes from the upstream (Mongolian) to downstream (Russian) part of the Selenga River basin. The geochemical fluxes experience considerable influence from Zaamar and Boroo mining areas, as well as Ulaanbaatar, Zakamensk and Ulan-Ude towns.