One of the most important problems of water management is the variation in the chemical composition of surface sources of drinking water under the influence ofvarious natural factors. Cyanotoxins, which are formed in basins due to the rapid utilization of inorganic nitrogen ammonium cations, nitrate and nitrite anions byblue-green algae (ammonium cations, nitrate and nitrite anions), cause the special attention among organic toxicants. The correction of algocenosis of thesebasins by plankton strains of Chlorella vulgaris IFR №С-111 green microalga is an innovation approach, which makes it possible to considerably decrease the contaminationlevel of basins by microtoxins. Our results obtained in 2013-2014 during the ecologic rehabilitation of medium natural basins contaminated by cyanotoxinsdemonstrated the improvement of chemical, biological, and organoleptic properties of water, which allows us to recommend this technology to prevent thecontamination of natural basins with cyanotoxins. These basins can be further used as the sources for preparing drinking water as well as for fish farming andrecreation purposes.