The species and spatial structure of the macrobenthos and pseudomeiobenthos communities in two lagoon ecosystems in Kislaya Bay area (Gulf of Kandalaksha, White Sea) is analyzed. All in all, 39 species of macrobenthos, 13 species of pseudomeobenthos organisms and 10 species of seagrasses and algae were found in the surveyed lagoon ecosystems. The lagoon located near Lake Ershovskoye contained more of brackish–water and marine euryhaline species of zoobenthos, whereas the more open lagoon had more of marine, less euryhaline macrobenthos species. The general indices of the macro- and pseudomeiobenthos community structure (total density and biomass) in the littoral zone were higher in the lagoon located near Lake Ershovskoye, which is explained by its greater siltation, lower impact of tides and currents in the lagoon, and hence more favorable conditions for development of numerous brackish-water and marine euryhaline macro- and pseudomeiobenthos species in the area. Statistical analysis showed that the strongest differences in the species composition, density and biomass of the macro- and pseudomeiobenthos community were observed between the upper-littoral and the lower-lying (lower- and mid-littoral) subzones. At the same time, the pseudomeobenthos community was more integrated compared to macrobenthos due to the spread of juvenile stages of Tubificoides benedii, Macoma balthica, Peringia ulvae throughout the littoral zone.