Species composition, structure, density and biomass of macrobenthos in the estuary of the Manuy River are described, its main communities are defined and their trophic characteristics, production, and distribution along the river channel are determined on the materials collected in July 2021. Three main biotopic zones of the estuary are identified by their hydrological features and parameters of macrobenthos: the river mouth, the lower estuary, and the upper estuary. Bilateral structure of salinity with 0.8–5.0 psu in the upper layer and > 27 psu near the bottom was observed in the lower estuary, whereas the upper estuarine zone was filled mostly by oligohaline water (0.8–1.6 psu), with only a thin refugial layer of the seawater (23.1 psu) at the depth of 0.9 m. In total, 24 species of benthic invertebrates and cyclostomes were presented in the macrobenthos. The species richness varied insignificantly across the estuary, from 4 species/section in its upper part to 9 species/section in the lower part, with lowered richness at the border between the lower and the upper estuarine zones, that corresponded to the theory of critical salinity. The density of macrobenthos distribution decreased from the river mouth to the boundary between the lower and upper zones (from 808.0 ± 162.0 ind./m2 to 16.0±2.8 ind./m2), then increased sharply in the upper estuary (up to 1384 ± 160 ind./m2). The total biomass had two peaks: in the lower estuary (4.381 ± 0.589 g/m2) and in the upper estuary (up to 28.950 g/m2), with the minimum of 0.076 ± 0.015 g/m2 between. The boundary between the meso-, polyhaline lower estuary and the oligohaline upper estuary had the width of several hundred meters. Four benthic communities were identified by various methods of cluster and ordination analysis, regardless of the method: two communities in the upper estuary (communities of Eogammarus kygi and Neomysis awatschensis), one community in the lower estuary (community of Hediste japonica) and the community of Haustorioides at the river mouth. Gathering detritivores formed the basis of biomass and macrobenthic production at the river mouth; collecting detritophages — sestonophages were the most significant in the lower estuary; while three key trophic groups were presented in the upper estuary: 1) collecting detritivores — macrogrinders — scavengers, 2) collecting detritivores, and 3) ground feeders — collecting detritivores. Daily production of macrobenthos was low at the river mouth and in the lower part of the lower estuary but increased in its upper part and in the upper estuary.