Organochlorine pesticides (OCPs) are characterized by ubiquity, bioaccumulation and persistence in the environment and are of worldwide concern. Sixteen surface sediment samples were analyzed for hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) to provide information on the levels, distribution and sources of these compounds after flood season in the old Yellow River Estuary, China. The concentrations of ΣDDT were considerably lower than those of ΣHCH. The concentrations of ΣHCH and ΣDDT in sediments after flood season were lower than those in sediments before flood season. The distribution indicated that the levels of HCHs and DDTs from sites near the beach were higher than those in the other sites. The principal component analysis suggested the usage of HCHs could serve as input sources for OCPs. The cluster analysis suggested that there were some similar migration characteristics and similar origins among these pesticides. O'p-DDT and o'p-DDT is of the greatest concern for the ecotoxicological risk.