Arctic marine ecosystems are undergoing rapid correction in response to multiple expressions of climate change, but the consequences of altered biodiversity for the sequestration, transformation and storage of nutrients are poorly constrained. Here, we determine the bioturbation activity of sediment-dwelling invertebrate communities over two consecutive summers that contrasted in sea-ice extent along a transect intersecting the polar front. We find a clear separation in community composition at the polar front that marks a transition in the type and amount of bioturbation activity, and associated nutrient concentrations, sufficient to distinguish a southern high from a northern low. Whilst patterns in community structure reflect proximity to arctic versus boreal conditions, our observations strongly suggest that faunal activity is moderated by seasonal variations in sea ice extent that influence food supply to the benthos. Our observations help visualize how a climate-driven reorganization of the Barents Sea benthic ecosystem may be expressed, and emphasize the rapidity with which an entire region could experience a functional transformation. As strong benthic-pelagic coupling is typical across most parts of the Arctic shelf, the response of these ecosystems to a changing climate will have important ramifications for ecosystem functioning and the trophic structure of the entire food web.