Chemical contaminant concentrations in wild organisms are used to assess environmental status under the European Marine Strategy Framework Directive. However, this approach is challenged by the complex intra- and inter-species variability, and the different regional features. In this study, concentrations in trace elements (As, Cd, Hg and Pb), polychlorinated biphenyls (PCBs), polychlorodibenzo-para-dioxines (PCDDs) and polychlorodibenzofuranes (PCDFs) were monitored in 8 fish species sampled on the continental shelf of three French regions: the Eastern English Channel (EEC) and Bay of Biscay (BoB) in the Northeast Atlantic Ocean, and the Gulf of Lions (GoL) in Western Mediterranean Sea. Our objectives were to identify species or regions more likely to be contaminated and to assess how to take this variability into account in environmental assessment. While concentrations were higher in benthic and demersal piscivores, PCB and PCDD/F concentrations (lipid-weight) were similar in most teleost species. For Cd, Hg and Pb, the trophic group accumulating the highest concentrations depended on the contaminant and region. Concentrations in Hg, PCBs and PCDD/Fs were higher in the EEC and/or GoL than in BoB. Cadmium and Pb concentrations were highest in the BoB. Lipid content accounted for 35%–84% of organic contaminant variability. Lipid normalisation was employed to enhance robustness in the identification of spatial patterns. Contaminant patterns in chondrichthyans clearly differed from that in teleosts. In addition, trophic levels accounted for ≤1% and ≤33% of the contaminant variability in teleost fishes in the EEC and BoB, respectively. Therefore, developing taxa-specific thresholds might be a more practical way forward for environmental assessment than normalisation to trophic levels.