To explore the riverine or atmospheric influence on the source–sink fates of typical persistent organic pollutants (POPs): polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in the large river estuary, atmospheric and seawater samples were collected simultaneously over a whole year at a remote small island in the Yangtze River Estuary (YRE), the East China Sea in 2013-2014.