As a byproduct of rapid urbanization and industrial development in the Pearl River estuary of South China, excessive release of various types of persistent toxic substances were conveyed from agricultural, industrial and municipal discharges at upstream section down into the estuary largely via various river outlets. In this paper, a persistent organic pollution (POP) characterization of sediments in the estuary is undertaken. More than one bioavailable toxicants are detected to play active roles in causing toxicity of marine sediments in the estuary. POPs may be transported for long distances to the downstream end of the Pearl River delta region. The data suggests that DDT might still be applied illegally within the region recently and that the prevalent levels of DDTs and HCHs in sediments are likely to pose detrimental biological effects on benthic organisms. The findings have significant implications in order to understand the environmental changes, to determine reasonable ways for future development, and to maintain a sustainable environment in the Pearl River estuary region.