Investigating the drivers of fish assemblage trophic structure is a critical question, in order to better understand ecosystem functioning, predict the effects of perturbations and implement integrated management of exploited marine ecosystems. Ecosystemic surveys enabled the determination of the trophic structure of the fish assemblages in three French marine ecosystems, namely the Eastern English Channel, the Bay of Biscay and the Gulf of Lions, through the simultaneous collection of qualitative (stable isotopes and energy content) and quantitative (biomass) data. In the Bay of Biscay and in the Gulf of Lions, pelagic primary production supported at least 80% of the fish biomass production, and explained the dominance of pelagic species, but with differences resulting from the different productivity. The lower productivity in the oligotrophic Gulf of Lions led to a lower total biomass, energy density as well as the predominance of zooplankton feeders. In contrast, fluxes in the Bay of Biscay were sufficient to support a higher biomass of pelagic piscivores, and of species with higher energy content. In the shallow Eastern English Channel, the respective contributions of pelagic and benthic sources were similar. Bentho-demersal species of higher trophic level dominated this assemblage, because of their ability to exploit both pathways. Results of the present study confirmed that fisheries-focused surveys can be used as efficient platforms to address questions about ecosystem functioning. Here it confirmed the expected differences between ecosystems and the importance of primary production and environment as drivers of fish assemblage structure and functioning. Future studies should nevertheless develop new methods to better assess the paramount role of low trophic level consumers.