Chemical contamination levels and stable isotope ratios provide integrated information about contaminant exposure, trophic position and also biological and environmental influences on marine organisms. By combining these approaches with otolith shape analyses, the aim of the present study was to document the spatial variability of Hg and PCB contamination of the European hake (Merluccius merluccius) in the French Mediterranean, hypothesizing that local contaminant sources, environmental conditions and biological specificities lead to site-specific contamination patterns. High Hg concentrations discriminated Corsica (average: 1.36 ± 0.80 μg g− 1 dm) from the Gulf of Lions (average values < 0.5 μg g− 1 dm), where Rhône River input caused high PCB burdens. CB 153 average concentrations ranged between 4.00 ± 0.64 and 18.39 ± 12.38 ng g− 1 dm in the Gulf of Lions, whatever the sex of the individuals, whereas the highest values in Corsica were 6.75 ± 4.22 ng g− 1 dm. Otolith shape discriminated juveniles and adults, due to their different habitats. The use of combined ecotracers was revealed as a powerful tool to discriminate between fish populations at large and small spatial scale, and to enable understanding of the environmental and biological influences on contamination patterns.