The south-eastern part of the Barents Sea, conventionally called the Pechora Sea, is among the most peculiar regions of the European Arctic. It is a shallow shelf area that is directly influenced by modified Atlantic and Arctic waters, as well as by freshwater runoff from the Pechora River. Due to its unique environmental features and habitats, the Pechora Sea is regarded as one of the most important areas of the Barents Sea. Rich planktonic and benthic communities, including extensive mussel beds, support large stocks of fish, seals, and walruses, and enormous gatherings of benthos feeding waterfowl. In recent years, economic activities, such as oil and gas production, shipping of crude oil through marine terminals, and ship traffic along the Northern Sea Route, have dramatically increased in the Pechora Sea. These anthropogenic pressures, as well as the observed and predicted natural environmental changes, will most likely affect the sea’s pelagic and benthic ecosystems. Therefore, information on the current state of the Pechora Sea ecosystems is urgently needed to provide baseline reference data, against which possible future shifts can be determined. The research presented in this special issue provides such data on the most important elements of the Pechora Sea ecosystems and adjacent areas and demonstrates the interconnection between these ecosystem components and key environmental factors. Considering the already recorded and potential changes in this region, the observed trends and processes in marine biota can be applied to other low Arctic seas and serve for modelling and predictions of future ecosystem shifts.