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Climate change and direct impacts of human activity are often considered among the main drivers of ecosystem dynamics; however, their relative importance for high-Arctic marine systems is not clearly understood. The Baydaratskaya Bay (southwestern part of the Kara Sea) was not subject to any human activity until 2011, when the construction of the underwater portion of a gas pipeline began; thus, it is a good place to investigate this issue. We used data on the macrobenthos from 1945 to 2013 to assess temporal variability and reveal either decadal-scale trends or construction impacts on the ecosystem. Until 2013, no evidence of long-term changes was detected in biomass, diversity, species composition, functional structure, and biogeographic attributes of the fauna. The ecological status was permanently evaluated as undisturbed. In 2013, however, an extensive shift occurred in the deep-sea area close to the pipeline trench. Benthic biomass and diversity decreased abruptly; while total abundance increased. The functional structure changed. Large bivalves almost completely disappeared, abundance of gastropods and amphipods dropped sharply, while the abundance of small opportunistic polychaetes increased abruptly. Benthic quality assessment indices indicated the deterioration of the community. The most likely reason for such catastrophic changes was the direct impact of dredging and dumping of sediments during pipeline burial from 2012 to 2013. We conclude that the benthic macrofauna in Baydaratskaya Bay has remained relatively stable over the last several decades without any signs of climate-driven borealization. Recent human activity, however, caused local but rapid and strong response, indicating the high sensitivity and vulnerability of this ecosystem.