The results of heavy metals monitoring in suspended substance and surface waters in the Kobdo River basin are described. The spatial distribution of metals in Kobdo River basin reflects influence of anthropogenous sources on catchments area. Steady exceeding of the background contents of mercury in surface waters is the result of influence of ore-body similar to mercury sulfide in Aktash settlement (the Republic Altai). Concentration of suspended parts of metals in natural waters in Kobdo River basin is near to the top value of the background contents for the not polluted waters.