Structural characteristics of benthic macroinvertebrate communities in mountain watercourses of different sizes have been studied in the Upper Ob basin. It has been found that species richness, diversity of zoobenthos, and most biotic indices in the background areas increase in the series from the smallest watercourses to large rivers. On the contrary, the values of the above parameters in areas polluted with mercury has proved to decrease, thereby indicating a significant transformation of the benthic communities. Approaches are proposed to select reference indices for assessing the ecological state of watercourses in the basin with regard to the size of the river, the structure of benthic communities, and variability of biotic indices along the background cross sections.