Polycyclic aromatic hydrocarbons (PAHs) were investigated in the marine ecosystem of the Daya Bay, South China. The PAH concentrations ranged from 340 to 710 ng/g dry weight in the sediments and from 110 to 520 ng/g wet weight in marine organisms, respectively. The dominant compounds were three- and four-ring PAHs in the sediments (53%–89%) and two- and three-ring PAHs in the marine species (67%–94%), respectively. PAHs mainly originated from both pyrolytic and petrogenic sources. Comparison with the effects-based sediment quality guideline values suggested that the ecological risk caused by the total PAHs was relatively low (less than 25% incidence of adverse effects) in the sedimentary environment. The median cancer risk level via seafood consumption (1.6 × 10− 5 for urban residents and 1.2 × 10− 5 for rural residents, respectively) was slightly higher than the maximum admissible level (10− 5) set by US EPA, but lower than the priority risk level (10− 4).