The protection of plants from diseases is mainly based on the use of chemical pesticides against pathogenic agents of fungal or bacterial etiology. That is why, in the past two decades, much attention has been paid to the development of ecological biological methods of combating plant diseases, which are considered an alternative to the traditional use of chemical pesticides. The aquatic environment is a good source for the detection of new strains of antagonistic microorganisms in relation to phytopathogens. The aim of the research was to determine the potential of the biodiversity of the microbiota isolated from the aquatic environment to combat the development of phytopathogenic fungi. Among actinobacteria, maximal inhibition of test cultures was achieved by strains of the genera Streptomyces (against A. alternata), Micromonospora (against A. niger), Actinoplanes, and Nocardia (against F. oxysporum). Bacteria of the genera Bacillus and Micrococcus possess the highest activity against A. alternata, B. cinerea, and F. oxysporum. The highest activity against phytopathogenic fungi was achieved by micromycetes of the genus Trichoderma (growth inhibition zones reached 40.0 mm). Cyanobacteria Oscillatoria brevis and Oscillatoria acutissima are active against A. niger and F. oxysporum, respectively. As a result, strains that were promising for use in phytosanitary control were discovered.