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The article is devoted to the study of the activity of radionuclides of natural and anthropogenic origin in the bottom sediments of the Pechora River delta lakes, which represent the largest river in the European sector of the Arctic Ocean Basin. The study revealed that the average activities of the radionuclides 137Cs, 210Pb, 226Ra, 232Th and 40K in the lake bottom sediments are 2.7, 22.6, 18.3, 25.4 and 535.9 Bq/kg, respectively. The mean values of total alpha and beta activities of the bottom sediments are 334.8 and 720.7 Bq/kg, respectively. These values are commensurate with the global average, thereby signifying a minimal level of natural and anthropogenic radioactivity in the Pechora delta lakes’ sediments. The data on physical and chemical parameters demonstrated that the flooded lakes of the Pechora delta are characterized by a relatively weak manifestation of sedimentation and biological processes. This is due to the hydrological regime of the delta (flooding of lakes during flood periods, daily tides) which prevents active accumulation of fine mineral and organic material in the lakes. The profound impact of hydrological conditions within the Pechora delta is evident in the disorderly vertical distribution of physico-chemical parameters and radionuclide activities across the depth of bottom sediment columns. The data obtained on radionuclide activities and physico-chemical parameters has enabled the estimation of the role played by flooded delta lakes as a component of the Pechora estuary system in the accumulation of pollutants. However, the vertical distribution of radionuclides in bottom sediments of these lakes has been found to be an unreliable indicator of the chronology of pollutant loads in the Pechora basin. This is due to the Pechora delta’s complex hydrological regime, which ensures the uneven flow of mineral and organic material into the lakes over time. The study of lake chronology is complicated by the manifestation of thermoabrasion (destruction) of lake shores, which is characteristic of permafrost development areas and which ensures the inflow of additional volumes of terrigenous material into lake basins.