This dataset gather isotope composition measured on organisms collected in Cap Caveau (Marseille, France) by SCUBA diving between 30 and 40 m depth from October to December 2015. A total of 78 compartments were analysed (76 taxa, POM and SOM). For each compartment or taxon, mean δ13C and δ15N values were calculated from 3 to 6 replicates. Isotope compositions are expressed in parts per thousand (‰) according to the equation: δX = [(Rsample/Rstandard) – 1] x 10^3, where X is 13C or 15N and R is the isotope ratio 13C/12C or 15N/14N, respectively