The biotesting of the level of genotoxicity and clastogenicity of deep and surface waters of Lake Sevan (Armenia) in the summer period was carried out using two test systems: of the model test object Tradescantia (clone 02) and phytoplankton. The Tradescantia clone 02 stamen hair mutations (Trad-SHM) and Tradescantia micronucleus (Trad-MCN) bioassays are two of the efficient and reliable biomonotory test systems for mutagenicity of air, water and soil polutans. Here we report a significant increase in the level of The Tradescantia clone 02 stamen hair mutations (Trad-SHM) somatic mutations in all investigated probes compared to phone control level. The maximum manifestation of these genetic effects – PC was observed in Gilli water samples with five-fold increase. According to the micronucleus test (Trad-MN), when studying its two main test-criteria: the percentage of tetrads with micronuclei and micronuclei in tetrads, the maximum frequency of test indicators was detected in water samples of Tsapatakh and Arpa, where their level was 4 times higher than the background. A significant positive correlation between the somatic mutation events and consentration of chemical elements Ca, K, Na, Mg, Fe, Mo (p<0.05; p<0.001) was revealed. It also showed a significant correlation between MN in tetrads and consentration of chemical elements Na, Ca, Fe, Mo, Ni, Cd (p<0.05). The analysis of the spatial distribution of phytoplankton in the water area of the Lake Sevan, as well as data on the abundance, biomass and composition of the dominant species in the summer observation period showed an intensive development of Cyanoprokaryota (HAB) and green algae in the all water area of the lake, which caused the process of its eutrophication.