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The article presents the results of a study of zoobenthos in streams in the Katon-Karagay national Park, carried out in 2009–2011. Presented are the taxonomic composition, a description of the spatial distribution of the given habitat classification of the studied small streams, and an area analysis of the fauna of amphibiotic insects of the studied area. An assessment of significance and metrics of zoobenthic communities for biological indication of the ecological status of the streams in the Bukhtarma river basin was carried out. Conducted research on anthropogenic load in unaffected rivers or sections of rivers will solve the problems associated with the lack of baseline data on the basin of the Bukhtarma river. Recommendations are given for the biodiversity conservation of stream bottom invertebrates in Protected Areas in the Altai-Sayan Ecoregion within Kazakhstan.