Hydrochemical and microbial monitoring of water systems in the Baikal region shows that microorganisms are indicators of anthropogenic pollution. High quality microorganisms were found in the bottom sediments of the Selenga River near populated areas. In the polluted sediment of Lake Baikal, the methanogenic community was replaced by a sulfidogenic one. The results obtained indicate the need for quantitative assessment of bacterial activity in the aquatic ecosystem during environmental monitoring.