Сurrently, the scientific research for methods to restore the quality of superficial water, including irrigation water, is actively advancing. The use of preparations of microbiological for intensification of the water system process purification is becoming increasingly common. In this aspect, it is advisable to expand the scientific search for the environmentally safe means of superface water purification in order to get quality irrigation water through the use of Bacillus subtilis microorganisms. Therefore, there is a need to investigate the environmental aspects of using Bacillus subtilis microorganisms in order to improve the quality of water, in particular, irrigation water. The aim of the research is to investigate the possibility of using Bacillus subtilis microorganisms to diminish the phytotoxicity of irrigation water. The water samples were tested before and after treatment with microorganisms (Bacillus subtilis) according to chemical indicators at the first stage. The treatment effiectiveness was as follows: BOI5 - 40%, suspended solids - 26%, COD - 37%, nitrite - 54%, ammonium nitrogen - 38%, manganese and lead - 56%, nitrate - 35%. After treatment with Bacillus subtilis, the water quality met the MPC norms for fisheries. At the next stage, the phytotoxic effect of the observed water samples before and after the treatment with Bacillus subtilis microorganisms (1:100 dilution) on germination of seeds, growth and root system of plants, was assessed. The effect of reducing toxicity was: root weight from 4% to 50%, with the least effect observed in the least polluted sample; root length from 48% to 65%, with the biggest effect observed in the most polluted water sample; length of aboveground part from 21% to 54%, without a connection to pollution in this case; weight of aboveground part from 25% to 46%, without a connection to pollution. The research found that after probiotic treatment, all water samples were classified as non-toxic by all biometric parameters. Definition the phytotoxicity of the roots, a clear correlation was observed between the increase in treatment effectiveness of Bacillus subtilis microorganisms and the increase in pollution levels. Thus, the effectiveness of using Bacillus subtilis microorganisms in order to reduce water phytotoxicity and improve irrigation water quality was found.