Ambient concentrations, congener patterns and multi-media distribution of PCDD/Fs and PCBs were determined in air, water, sediment and mussels in a semi-enclosed marine ecosystem (Thau lagoon, France). ∑2,3,7,8-PCDD/F and ∑7ICES PCB air concentrations (0.2–1.4 and 31–57 pg m −3, respectively) were typical of rural areas. Concentrations in the water column were very low for PCDD/Fs (163–476 fg L −1) and low for PCBs (138–708 pg L −1). PCDD/F and PCB concentrations found in surface sediment (0.15–1.6 and 2.5–33 ng g −1 d.w., respectively) and mussel (13–21 pg g −1 d.w. and 10–39 ng g −1 d.w., respectively) were medium levels. PCDD/F congener patterns observed in air, water particulate phase and sediments were similar suggesting direct coupling among these compartments and atmospheric inputs of PCDD/Fs into the lagoon. Conversely, for the same set of samples, similar patterns were not observed for PCBs in the mentioned compartments. Multi-media ambient concentrations and distribution of PCDD/Fs and PCBs in Thau Lagoon provide insight into the POPs behavior in semi-enclosed marine ecosystems.