Surface sediment samples were collected from the Yangtze River Estuary (YRE) to the inner-shelf mud area of the East China Sea (ECS) for a comprehensive study of the sources and fates of polychlorinated biphenyls (PCBs) based on their spatial distribution, deposition flux, and mass inventory. The total concentrations of 32 PCBs (Σ32PCBs) varied from 0.3 to 11.9 ng/g dry weight. Under strong hydrodynamic conditions, the weak correlations between TOC or MD and Σ32PCB concentrations were observed in the YRE. In contrast, there were relatively well relationships of PCBs with TOC content and sediment grain size in the inner shelf of the ECS due to the influence of hydrological sorting from the YRE to the inner shelf of the ECS. This suggests that the Yangtze River input plays a considerable role in controlling the distribution of PCBs in the coastal ECS. Compared with the annual discharge of Σ32PCBs from the Yangtze River to the sea (3.21 t/yr), the deposition flux was estimated to be ~2.63 t/yr. Furthermore, a total mass inventory of 50 tons in the sediments suggests that the YRE and inner shelf mud of the ECS represents an important global sink of PCBs. Estimated 21–39% of sedimentary PCBs were derived from local emissions (mainly dismantling of electronic waste) aside from Yangtze River input. Higher proportions of pentaCBs were also observed near the central Zhejiang Coast, providing further evidence that the local emission from e-waste dismantling near the coast is a significant contributor to sedimentary PCBs in the coastal ECS.