Emergency situation in summer 2013 due to flooding of extensive areas of the Russian Amur-River territories (including residential areas with different level of development of public services and amenities, agricultural land, sites of cattle grazing and stock-keeping) resulted in the increased microbiological, virologic and physical-chemical load upon water reservoir ecosystems. The results of monitoring over water supply sources, quality of drinking water and surface reservoir waters in the devastated territories were analyzed by the specialists from Rospotrebnadzor and specialized anti-epidemic teams No. 1 and 2. Complex approach presuming increase in extent and frequency of the examinations, performance of operative epidemiological analysis along with daily adequation of preventive and anti-epidemic measures allowed for taking control over the situation and to avoid epidemic complications as regards acute water-borne intestinal infections.