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Macrobenthic communities have been routinely used as indicators of changing environment. Such studies are of current interest in Arctic since global climate change and human activities can lead to significant biotic alteration of the region. Though examples of long-term changes in benthic community structure are numerous, it is still hard to identify whether such changes are driven by natural spatio-temporal variability, climate shifts or by direct anthropogenic impacts, or by a combination of all these factors. Baydaratskaya Bay is situated in the southwestern part of the Kara Sea. It is characterized by the low level of freshwater runoff and long ice-coverage period. The area suffered from relatively low anthropogenic activity up to the year 2011, when the seafloor pipeline laying-out began across the bay (the Yamal-Center gas pipeline project). We used the data obtained during six surveys at 1992-2013 and the archive data from the 1946 year expedition to trace the natural and human-influenced changes in benthic communities. The results showed that benthic community structure was significantly influenced by the depth, and three assemblages could be clearly distinguished occupying different depth ranges (shallower 10 m, 10-20 m, and deeper 20 m, respectively). For each of the assemblages, the composition of dominant species, as well as the integral parameters (total biomass and abundance, species diversity, ABC-index) remained quite stable during the whole period of investigation, except for the deepest (over 20 meters) stations 2013. This group of stations showed significant changes at 2012- 2013 years, then the total biomass, mean individual weight and species diversity decreased sharply. In 2013, the absence of large bivalves and increased abundance of small polychaetes had been recorded at these stations. It is more likely that just the recent human activity (dumping of dredged sediments) caused these local but considerable changes in the benthic communities, while their structure remained stable during the past decades.