This article provides information on the identification of micromycetes found in samples taken from areas of transboundary rivers of Azerbaijan with different levels of anthropogenic impact, and the study of their role in the removal of pollutants. Certain micromycetes were used as indicators of water quality. As a result of the studies, micromycetes belonging to 38 species from 16 genera were identified. Directly at the sampling site, water temperature, pH, and the amount of dissolved oxygen in the water were measured, and biogenic elements were determined in laboratory conditions. The presence of nutrients in the studied river waters showed variable results. Thus, in the Astarachay River, nitrites range from 0.01–0.02 mg/l, nitrates 0.56–0.70 mg/l, ammonium 0.5–1.50 mg/l, phosphates 0.00–0.01 mg/l. In the Bolgarchay River, these indicators for nitrite range from 0.02–0.05 mg/l, for nitrates 0.20–0.50 mg/l, for ammonium 0.10–0.44 mg/l, for phosphates 0.01–0.05 mg/l. In the Arazchay River, nitrites range from 0.01–0.83 mg/l, nitrates 0.08–7.40 mg/l, ammonium 0.05–3.57 mg/l, phosphates 0.05–0.94 mg/l, and in Okhchuchay these indicators for nitrite range from 0.09 to 0.71 mg/l. l, nitrates 0.68–6.00 mg/l, ammonium 0.23–6.45 mg/l, phosphates 0.09–0.65 mg/l. The results obtained showed that the identified microscopic fungi are involved in the formation of rich flora as an adaptation in river waters. The biomass and number of micromycetes significantly depend on hydrochemical conditions: parameters such as temperature, dissolved oxygen, pH, forms of nitrogen, phosphorus and organic carbon fractions. It can be recommended to use mushrooms for biological control of surface water purity and sanitary safety. It should be noted that environmental factors also influence the diversity of micromycetes