In order to assess the current state of the ecosystem by hydrobiological indicators, studies were conducted on the Island of Kizhi in Lake Onego (in the buffer zone of the World Heritage Site ‘Kizhi Pogost’ (C544)) during the growing season of 2023. The morphology of bacterioplankton had spatial and seasonal variability. High numbers of conditionally pathogenic microorganisms were typical of the western coast of Kizhi Island, which is characterized by low water exchange. As a result of the phytoplankton survey, structural and quantitative indicators pertaining to phytoplankton development in the area of Kizhi skerries and the background station were obtained. In general, quantitative indicators of microalgae characterise the area as mesotrophic. Based on the indicator values of phytoplankton and their quantitative development, the type of waters in the area of Kizhi Island can be referred to the β-mesosaprobic pollution zone. Based on the data analysis for the growing season 2023, it was noted that the zooplankton species composition and dominants of the Kizhi skerries area and the central lake area are typical for large lakes of North-West Russia. High species diversity characterises planktonic systems as oligotrophic. During the vegetation period, zooplankton trophic level indices in the Kizhi Skerries area varied from oligotrophic (in autumn) to α-eutrophic (in spring). The trophic level in the central part of the lake during the vegetation period corresponded to the ultraoligotrophic-oligotrophic. Analysis of macrozoobenthos current state did not reveal any differences in quantitative indicators of the Kizhi Island area and the central part. The average benthos biomass in the skerries varied from 0.44 to 2.5 g/m2, which corresponds to the oligotrophic state. In the central part, the average biomass was 0.99 g/m2, which corresponds to an ultraoligotrophic status.