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This paper examines impacts of physical and geographic settings of the Arctic seas on the directions of the suspended substance transport within water areas. The cumulative effect of the hydrological factors, such as current directions, with geomorphic features of the region, e.g. the seabed bathymetry or beach types, has strong impact on the direction of the substance distribution within water bodies, and in turn, to biota sustainability. Additionally to the contamination caused by anthropogenic sources, the oceanological factors determine the risk of water pollution by chemicals. Current research contributes towards regional studies of Arctic ocean. It studies interrelationships of multiple factors on environmental sustainability of the marine ecosystems.