Abstract An attempt has been made using the molecular signatures of anthropogenic persistent organic chemicals such as DDTs and PCBs and sterol biomarkers in suspended particulate matter (SPM) to verify certain biogeochemical postulations, especially the origin of low salinity water mass and SPM in a river plume ecosystem in the Yellow Sea. This investigation was also assisted by satellite imagery using SeaWiFS and concurrent measurement of salinity. The target chemicals were measured in SPM, sampled near Yangtze River mouth to stations that were close to Jeju Island, Korea. ΣDDTs and ΣPCBs in SPM were at ultra trace levels (parts-per-quadrillion) ranging from 3.3 to 39 and from 20 to 68 pg L −1, respectively; while Σsterols occurred from 3200 to 32,000 pg L −1 range. The spatial distribution and molecular compositions were studied. This study illustrated the effectiveness of unconventional molecular tracers in identifying water masses and movement of riverine plumes to regional seas in the transport of sediments and contaminants. Additionally, it highlighted the importance of long range-longitudinal transport of contaminants (transboundary pollution) in regional seas and their impact on the ecosystem.