The Environment Protection Department of Hong Kong has a monitoring program for persistent organic contaminants in sediments of Victoria Harbour, the main harbour of Hong Kong. A fugacity model has been used, based on this sedimentary data, to estimate inputs to the system (probably from sewage, stormwater and industrial discharges) as well as the fate of the contaminants, particularly in terms of the aqueous and biotic concentrations. The risk of deleterious effects on the natural marine system, as well as on the consumers of seafood from the system, was carried out using the estimated aqueous and biotic concentrations together with accepted environmental quality guidelines. The result of our analysis indicated that the chlorohydrocarbons, PCBs (as Aroclor 1254) total DDT and total HCH pose a significant risk, and probably have caused damage to the marine ecosystem as well as posing a hazard to seafood consumers. Much higher concentrations of the less toxic total alkanes, nonaromatic hydrocarbons, linear alkyl benzenes and the compounds giving a unresolved complex mixture (UCM) cannot be evaluated due to a lack of environmental guidelines and the complexity of these substances. However, it is probable that these substances add adverse effects to those due to the other contaminants.