Ecopath mass-balanced models are widely-used tools to address various challenges in the understanding and protection of ecosystems. To track the continuing improvements in data and the evolving environment (climate change, anthropic pressure), new models are regularly being developed. In this study, we built a Gulf of Lion Ecopath model, focused on the continental shelf, featuring enhanced representation of benthic invertebrates and a realistic assessment of catches, and which takes into account the significant changes observed after 2008–2009 in the trophic structure of this ecosystem as well as related changes in fisheries activities. The model is composed of 68 functional groups, including 6 primary producers, discards and detritus, 27 invertebrate groups, 31 fish groups, dolphins and seabirds. New datasets were taken into account for biomasses, as well as for diets. P/B and Q/B parameters were calculated to include the most recent and geographically closest data. Model results highlight a food web diagram, ranging over 5 trophic levels and placing Prionace glauca, Squalus acanthias and dolphins as top predators. The mixed trophic impact analysis showed that the groups with the highest accumulated negative impacts are, in decreasing order, benthic trawls, nets and carnivorous echinoderms. The groups with the highest accumulated positive impacts are, in decreasing order, detritus, microphytoplankton and nanoplankton. The flux analysis shows that a major part of the flows occurs at trophic level 2 with 35.1% of the model total throughput and 43.8% of the total biomass. The catches have a mean trophic level of 3.47, higher than in previous studies, reflecting the changes in the fisheries activities.