Under climate change, future species assemblages will be driven by the movements and poleward shift of local species and the arrival of more thermophilic species from lower latitudes. To evaluate the impacts of climate change on marine communities in the Bay of Biscay, we used the hierarchical filters modelling approach. Models integrated 3 vertical depth layers and considered 2 Intergovernmental Panel on Climate Change (IPCC) scenarios (Representative Concentration Pathway, RCP2.6 and RCP8.5) and 2 periods (2041-2050 and 2091-2100) to simulate potential future species distributions. Results predicted potentially suitable future ranges for 163 species as well as future arrivals of non-indigenous southern species. We aggregated these results to map changes in species assemblages. Results revealed that coastal areas would undergo the highest species loss among the Bay of Biscay species, depending on their vertical habitat (benthic, demersal, benthopelagic or pelagic). Benthic and demersal species were projected to experience a westward shift, which would induce a deepening of those species. In contrast, pelagic species were projected to shift northward. The potential ecological niche for half of the studied species, mostly benthic and demersal, was projected to decrease under climate change. In addition, a high rate of southern species arrivals is expected (+28%). Assessment of community composition showed high species replacement within the 0-50 m isobath, driven by the replacement of native species by southern ones. This could lead to a major reorganization of trophic networks and have socio-economic impacts.