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Recent Arctic warming has major influences on biological communities, especially in freshwater environments. There is substantial evidence that lake ecosystems in the Canadian Arctic and Fennoscandia are undergoing changes that have been linked to human-induced climate warming during the past 150–100 years. However, only few data linking recent climatic changes with the changes in biological communities are available from the Russian Arctic. We investigated a short sediment core (bottom of the core dates to 1830 CE) from Lake Bolshoy Kharbey, the biggest lake of the Bol`shezemelskaya Tundra, western Russian Arctic, using chironomid, cladocera, diatom and palynological analyses. Variations in biological proxy were linked to regional meteorological data and compared with the available sub-recent palaeoecological and hydrobiological studies from the region. The overall change in species composition was the smallest for terrestrial vegetation (0.485 SD) followed by cladoceran communities (0.966 SD). Chironomid taxonomic turnover was 1.331 SD, and the greatest rate of change was observed in diatom assemblages (1.701 SD). Changes in biological communities demonstrated a correlation with meteorologically recorded climatic parameters (air temperature and precipitation). The strongest taxonomic shifts in biological communities took place in 1880 and 1980. Both dates can be linked with prominent and recent climatic events: 1880 can be related to the end of the Little Ice Age in the region and 1980 is the beginning of the modern accelerating warming.