One hundred forty-three surface sediment (0–5 cm depth) samples were collected from locations representing industrialized areas, less-industrialized areas, and e-waste recycling areas in the Pearl River Delta (PRD). The spatial distribution of polychlorinated biphenyls (PCBs) and their potential adverse effects on aquatic organisms were investigated. The average PCB concentration in the less-industrialized areas (background) in the PRD was approximately 10 ng/g dry weight (dw), which was generally half that found in the industrialized areas (approximately 22 ng/g dw). Severe PCB contamination, with concentrations ranging from 1000 to 26500 ng/g dw, was found in pond sediments collected from e-waste recycling areas. It is very likely that such contamination would have had adverse effects on the aquatic biota there. PCBs in the e-waste recycling areas were dominated by penta- and hex-PCB congeners, which made them significantly different from those found in other regions, where tri- and tetra-PCB congeners were predominant. Higher abundances of less chlorinated congeners were seen in the less-industrialized areas compared to the industrialized areas. Differences in the transport abilities of different congeners, together with dechlorination of higher chlorinated congeners, is the most likely reasons for this.