Aquaculture wetlands, particularly those located within urban areas, are fragile ecosystems which are generally heavily impacted by urban and aquaculture activities. However, there are, to date, no reports on adverse effects related to polycyclic aromatic hydrocarbons (PAHs) in sediments from aquaculture wetlands in metropolitan areas. The characterization, sources, and incidence of adverse effects on aquatic biota of PAHs were studied in the riverine and estuarine sediments of the Rongjiang River in an aquaculture wetland in Chaoshan metropolis. The total PAH concentrations varied from 46.0 to 1665.2 ng/g (dry weight), with a mean of 246.4 ng/g, indicating lower concentrations than those of other comparable rivers and estuaries worldwide. High-molecular-weight PAHs were the major PAH species, with fluorene, benzo(b)fluoranthene, and benzo(a)pyrene as the dominant components. These PAHs are likely to be mainly derived from oil and coal/biomass combustion. Probability risk assessment indicated a moderate PAH ecological risk in the Rongjiang River and its estuary (RJE). Accordingly, a comprehensive management plan should be established to ensure sustainable aquaculture wetlands.