Polycyclic aromatic hydrocarbons (PAHs) cause environmental and human health risks. We compared PAHs in sediment from the Yangtze (YRE) and Pearl River Estuaries (PRE). Ecological risks in both estuaries are moderate, and higher in PRE than YRE. Risk of cancer from contact with the sediment is low to moderate in both estuaries. Control measures should be carried out to reduce or eliminate these risks.