Water of Selenga River from the border with Mongolia to its delta was analyzed for some microbiological indicators. The data obtained demonstrate that the waters of Selenga tributaries are cleaner as compared with the river itself. On all 14 sampling stations except the station situated upstream from Ust-Kyakhta E. coli was detected. Low water level of the river determined high indicators of total number of bacteria – 4,32·106 – 11,37·106 cell/ml. Almost a half of the samples demonstrated denitrification activity of microorganisms which indicates to self-purification process of the water body.