In modern conditions of Gorny Altai, with an increase in anthropogenic load on the ecosystems of the region, it becomes important to assess environmental pollution. The state of the environment monitoring is a topical direction of science. The work analyzes the distribution and structural features of macrozoobenthos communities in the rivers of Altai. Revealed 25 species of invertebrate aquatic organisms belonging to 4 types and 6 classes. Benthic communities of 12 different water bodies of the Northern and Central Altai have been analyzed. Analysis of the studied structure of groups based on Euclidean distances for the shares of species in communities showed that they can be divided into three classes depending on the dominant species in them. The scheme based on the Jaccard index made it possible to reveal the influence of environmental factors that determine the structure of macrozoobenthos communities in Altai rivers. It was revealed that the anthropogenic factor has an indirect effect on the structure of communities of aquatic organisms; therefore, the macrofauna of aquatic organisms can be used as a primary indicator of the state of aquatic ecosystems.