Zapovednik (Nature Reserve) “Yuganskiy” - is a large Western Siberian protected area situated in the Bolshoy Yugan River basin (Middle Ob Basin). Though usually the biological investigations in nature reserves are restricted to terrestrial ecosystems, the study of the aquatic biota is also very important. Of a significant value is the study of intact freshwater ecosystems that would be destined to be highly influenced in future especially by the oil and gas industry of Western Siberia. The bottom invertebrates inhabiting streams and lakes play an important role in the functioning of the freshwater communities. In this paper, some results of investigations of the macrozoobenthic community of the Bolshoy Yugan River basin are presented. Two rivers, Bolshoy Yugan and Negusyah, were explored from May to September of 2011. The hydrobiological transects were established in the Zapovednik itself, its Protected zone and adjacent area. The standard methods of sampling and laboratory treatment of benthic samples were used. The Petersen’s bottom dredge with capture area of 0.025 m 2 was used. In total, 120 samples of benthic animals were taken. The macrozoobenthos of the studied rivers consist of 21 taxons of invertebrate animals, in the Bolshoy Yugan River - 16 taxons and in the Negusyah River - 21 taxons. In both rivers, chironomid larvae and bivalves of the superfamily Pisidioidea dominate. The density of macrozoobenthos in the Bolshoy Yugan River during the ice-free period changed from 51 to 1280 ind./m 2 and the biomass changed from 0.1 to 4.5 g/m 2. In the Negusyah River the density changed from 0.6 to 4.5 thousand ind./m 2 and the biomass changed from 1.0 to 24.9 g/m 2. Fluctuations in the density of macrozoobenthos were most pronounced in the hydrobiological transect No. 3 of Negusyah River. A similar fluctuation has been observed in the first transect. The 2-4 transects have shown biomass decrease in July and August. The taxonomic composition of macrozoobenthos during the ice-free period proved to be more stable measure than density and biomass. The main reasons for fluctuations of diversity, density and biomass of aquatic invertebrates are peculiarities of hydrological regime of rivers and life cycles of dipteran insects and bivalve mollusks. These data represent the first time study of the diversity, density and biomass dynamics of the macrozoobenthos of the rivers Bolshoy Yugan and Negusyah during the ice-free period (May-September).