Mercury (Hg) is a global threat for marine ecosystems, especially within the Mediterranean Sea. The concern is higher for deep-sea organisms, as the Hg concentration in their tissues is commonly high. To assess the influence of food supply at two trophic levels, total Hg concentrations and carbon and nitrogen stable isotope ratios were determined in 7 species (4 teleosts, 2 sharks, and 1 crustacean) sampled on the upper part of the continental slope of the Gulf of Lions (Northwestern Mediterranean Sea), at depths between 284 and 816 m. Mean Hg concentrations ranged from 1.30 ± 0.61 to 7.13 ± 7.09 μg g− 1 dry mass, with maximum values observed for small-spotted catshark Scyliorhinus canicula. For all species except blue whiting Micromesistius poutassou, Hg concentrations were above the health safety limits for human consumption defined by the European Commission, with a variable proportion of the individuals exceeding limits (from 23% for the Norway lobster Nephrops norvegicus to 82% for the blackbelly rosefish Helicolenus dactylopterus). Measured concentrations increased with increasing trophic levels. Carbon isotopic ratios measured for these organisms demonstrated that settling phytoplanktonic organic matter is not only the main source fueling trophic webs but also the carrier of Hg to this habitat. Inter- and intraspecific variations of Hg concentrations revealed the importance of feeding patterns in Hg bioaccumulation. In addition, biological parameters, such as growth rate or bathymetric range explain the observed contamination trends.