New Caledonia is one of the main hot spots of biodiversity on the planet. Large amounts of contaminants are discharged into the lagoon as a result of increasing anthropogenic activities such as intense mining, urbanization and industrialization. Concentrations of 14 trace elements and 26 persistent organic pollutants (POPs: PCBs and pesticides) were measured in the muscles of two anguilliform fish species, over a coast to barrier reef gradient in two lagoon areas differently exposed to anthropic disturbances. This study emphasizes the high trace element contamination status of anguilliform fish and also highlights slight but perceptible organic pollution. The contamination extends throughout the lagoon, from coast to barrier reef, even in areas remote from emission points. High levels of trace elements, especially those linked to mining activities (i.e. Co, Cr, Fe, Mn and Ni), were detected in coastal sites. Furthermore the large dispersion of most POPs throughout the entire lagoon poses the question of their potential toxicity on marine organisms from numerous habitats. Our results underline the need for long term monitoring of various contaminants over large spatial and time scales.