Although the Bay of Biscay is an ecoregion with a long history of fisheries exploitation, it is also influenced by climate change that affects ecosystem structure and trophodynamics. In this study, using a linear inverse model based on a Monte Carlo-Markov Chain approach (LIM-MCMC) and an Ecological Network Analysis (ENA), we assess the trophic status of this region under different scenarios of climate change (IPCC scenarios A1B, A2 and B2)). More precisely, we will estimate the potential consequences of climate-driven alterations of fish compartments on (1) other trophic compartments, and (2) on the food-web structural properties. A first set of scenarios of climate-driven alterations of fish compartments came from a multispecies individual-based model (OSMOSE) applied in the Bay of Biscay. The OSMOSE model estimates the biomass dynamics of main exploited fish species together with associated processes (e.g. growth, respiration, mortality) from the outputs of the biogeochemical model ROMS-N2P2Z2D2 (i.e., predator/prey possibility of co-occurrence and compatibility between predators’ and preys’ sizes). A second set of climate-driven alterations of fish compartments is provided by the Non-Parametric Probabilistic Ecological Niche (NPPEN) model, predicting probabilities of occurrence based on species ecological niches sensu Hutchinson from key environmental factors. The coupling of LIM-MCMC with ENA allows statistical comparisons of food web properties to be investigated.