3D coupled modeling approach is used for the PCB dispersion assessment in the Gulf of Lion and its transfer to zooplankton via biogeochemical processes. PCB budgets and fluxes between the different species of PCB: dissolved, particulate, biosorbed on plankton, assimilated by zooplankton, which are governed by different processes: adsorption/desorption, bacteria and plankton mortality, zooplankton excretion, grazing, mineralization, volatilization have been estimated. Model outputs were compared with the available in situ data. It was found that the Rhone River outflows play an important role in the organism contamination in the coastal zone, whereas the atmospheric depositions are rather more important in the offshore zones. The transfer of the available contaminant to bacteria and phytoplankton species is mainly related to the biomass present in the water column. Absorption fluxes (grazing) to zooplankton are rather higher than the passive sorption fluxes, which are themselves also linked to the sorption coefficient.