Cyanobacteria, which develop abundantly in aquatic ecosystems, can be harmful to humans and animals not only by releasing toxins that cause poisoning but also by provoking cytogenetic effects. The influence of the mass development of cyanobacteria on the genotoxic properties of natural water has been studied in model ecosystems (microcosms) with different compositions of biotic components (zooplankton, amphipods and fish). The validated plant test system “Allium test” was used in this study. Genotoxic effects were detected at microcystin concentrations below those established by the World Health Organization (WHO) for drinking water. In all experimental treatments, cells with disorders such as polyploidy and mitotic abnormalities associated with damage to the mitotic spindle, including c-mitosis, as well as lagging chromosomes were found. Genotoxic effects were associated with the abundance of cyanobacteria, which, in turn, depended on the composition of aquatic organisms in the experimental ecosystem. Fish, to a greater extent than other aquatic animals, maintain an abundance of cyanobacteria. After one month, in microcosms with fish, mitotic abnormalities and polyploidy continued to be detected, whereas in other treatments, there were no statistically significant genotoxic effects. In microcosms with amphipods, the number and biomass of cyanobacteria decreased to the greatest extent, and only one parameter of genotoxic activity (frequency of polyploidy) significantly differed from the control.