Due to its extensive continental shelf, the Gulf of Lion, situated in the northwestern Mediterranean Sea, plays a crucial role in providing ecological services amidst various natural and anthropogenic pressures. Exposed to the impacts of climate change and suitable for marine energy development projects, the conservation of marine biodiversity in this environment raises significant concerns. To detect any potential disturbances in the functioning of the terrigenous mud community on the continental shelf, we conducted stable carbon and nitrogen isotope analyses on suspended particulate organic matter, sediments, and benthic fauna. Since seasonality is a structuring factor for the functioning of such an oligotrophic ecosystem, we conducted two sampling campaigns in 2018 to capture contrasting scenarios of water column stratification-one in April during well-mixed conditions and high phytoplankton production, and another in September at the end of the summer thermal stratification period characterized by low primary productivity. Stable isotope analysis revealed changes in the structure of the benthic food web in response to seasonal stratification of the water column. While isotopic niches of taxa remained evenly distributed, the total niche space contracted between sampling dates, primarily affecting low trophic level consumers. The observed contraction aligns with that reported at the base of the pelagic food web. These results enhance our understanding of the functioning of the continental shelf of the Gulf of Lion. The intense trawling pressure on the study site affected sampling. In this context, this research contributes not only to the knowledge of seasonal trophic variations but also provides a reference state to understand the future of this Mediterranean continental shelf.