Polycyclic aromatic hydrocarbons (PAHs) have two or more benzene rings, are persistent in the environment, and are carcinogenic, teratogenic, and mutagenic to most organisms, including humans. We evaluated the distribution and source of PAHs near Lingdingyang in the Pearl River Estuary. We measured the concentration of sixteen polycyclic aromatic hydrocarbons (PAHs) in the surface sediments collected at 20 sites in June, 2010 using GC-MS. We detected 15 PAHs at all sites, but the distribution of the remaining PAHs was uneven. Concentrations ranged from 143.9–522.67 ng/g (mean: 287.05 ng/g), and were not particularly high when compared with other developed areas throughout the world. The highest levels occurred near the NanSha port of GuangZhou and Shenzhen Baoan district. This is likely due to discharge from logistics, oil, and auto manufacture. The PAHs were divided into five groups based on the number of rings (maximum = 3). We used the isomer ratios (e.g., phenanthrene/anthracene and fluoran- thene/pyrene) to assess the origins of PAHs. The ratio of fluoranthene/pyrene was below 1 at 85% of sites, suggesting that the contribution of petroleum to PAHs was high, and that coal fuel combustion contributed relatively little. To confirm this, we used the Pyr/B(a)P ratio method and obtained similar results. We used the low-mid level of the effect range and the quotient of the mid-value of the mean effect to assess the ecological risk. Our analysis suggests that the risk to organisms is small if the PAH content is lower than the ERL. However, if the PAH content is between the ERL and ERM, there may be some risk and if the content is >ERM, the risk is high. The levels of two PAHs (Ace and Fl) were between the ERL and ERM at three sites. All other PAHs were below the ERL, so posed little risk. We detected high molecular weight PAHs [I(1,2,3)P] at 9 sites. These PAHs have no minimum safety value so likely pose a risk to organisms living at these sites. All MERM-Q values were below 0.1 indicating that the risk was low at all sites.