A screening of relevant biomarkers was carried out in order to evaluate metabolic and cellular damages in European eels exposed to a non-point source contamination by persistent organic pollutants (POP) such as polycyclic aromatic hydrocarbons (PAH) and organochlorine compounds (OC) in a protected area, the Nature Reserve of Camargue (France). Investigations were focused on metabolic responses including detoxification mechanisms (biotransformation, antioxidant process), energy requirements and enzymatic membrane markers either involved in neuronal conduction (acetylcholinesterase, AChE) or in osmoregulation and energy metabolism (ATPases). The hepatic and muscular glycogen rates seemed to be suitable biomarkers as well as three hepatic activities involved in the protection against oxyradicals: catalase, glutathione peroxidase (SeGPx) and superoxide dismutases (SOD). The muscle and gill ATPases as well as the muscle and brain AChE showed more significant relevance in terms of biomarkers than the biotransformation enzymes: ethoxyresorufine-O-deethylase (EROD) and uridine diphospho-glucuronyl transferase (UDPGT). However, most of these enzymatic activities depend on numerous abiotic factors, which must be taken into account in such a biomarker assessment approach. Our study provides some conclusive elements to approve the use in situ of biomarkers developed from laboratory studies. It also raises a question regarding the location of contaminant impregnation in fish organ, in relation with age, development status or mode of contamination, and its influence on biomarker response. If the relevance of membrane indicators is confirmed, this study provides an original statement of the extent of the ecotoxicological threat for the aquatic species in a protected area, due to the occurrence of POP in the cell membranes.