Protecting Arctic ecosystems against potential adverse effects from anthropogenic activities is recognized as a top priority. In particular, understanding the accumulation and effects of persistent organic pollutants (POPs) in these otherwise pristine ecosystems remains a scientific challenge. Here, we combine more than 20 000 tissue concentrations, a food web bioaccumulation model, and time trend analyses to demonstrate that the concentrations of legacy-POPs in the Barents/Norwegian Sea fauna decreased 10-fold between 1985 and 2010, which reflects regulatory efforts to restrict these substances. In contrast, concentrations of fossil fuel derived PAHs in lower trophic levels (invertebrates and fish) increased 10 to 30 fold over the past 25 years and now dominate the summed POP burden (25 POPs, including 11 PAHs) in these biota. Before 2000, PCBs dominated the summed POP burden in top predators. Our findings indicate that the debate on the environmental impacts of fossil fuel burning should move beyond the expected seawater temperature increase and examine the possible environmental impact of fossil fuel derived PAHs.