Submarine canyons are regarded as a sink for pollutants. In order to determine if this theory applied to deep-sea species from an important fishing ground (the Blanes submarine canyon) located in the NW Mediterranean, we sampled the commercial fish Phycis blennoides and Micromesistius poutassou and the crustacean Aristeus antennatus. Specimens were sampled inside and outside (in the open continental slope) the submarine canyon; both are regarded as potentially affected by exposure to different anthropogenic chemicals. Several pollution biomarkers in muscle (activity of cholinesterases) and liver/hepatopancreas (catalase, glutathione S-transferases, carboxylesterases, ethoxyresorufin O-deethylase in fish or mixed function oxygenase (MFO)-related reductases in crustacean, and lipid peroxidation levels) were measured. Chemical analysis of the persistent organic pollutants, namely polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) was also performed on the fish and crustacean muscle. Biomarker activities and levels were discussed in relation to pollutant exposure, habitat, and parameters including sex, size, and species. Biochemical responses and chemical analysis of PCBs evidenced interspecies differences as well as sex and size-related ones, mainly in A. antennatus. An indication of higher exposure to pollutants inside the canyon was observed, which was more clearly reflected in the fish than in the crustacean. However, further research is required to confirm this observation.