Surface sediment samples from Bohai Bay and its adjacent river, China, were analyzed for aliphatic hydrocarbon, PAHs and biomarkers in order to determine the distribution, composition and source of organic matter in a coastal environment. Results suggested that the input of organic matter from anthropogenic activities has a more significant influence on its distribution than that from natural processes. Petroleum contamination, mainly from offshore oil exploration and discharge of pollutants from rivers, was the main source of n-alkanes. PAHs were mostly of pyrogenic origin; while some sites in Yellow River Estuary were derived mainly from the petrogenic sources. The toxic assessment suggested that the PAHs in surface sediments will not cause immediately adverse biological effects in sediments from Bohai Bay and its adjacent river, China.