The integration, accumulation and transfer of trace elements across the main tropic levels of many food webs are poorly documented. This is notably the case for the complex trophic webs of coral reef ecosystems. Our results concerning the south-west lagoon of New Caledonia show that both abiotic (i.e. sediments) and biotic (i.e. primary producers, consumers and predators) compartments are generally contaminated by trace elements. However, our analyses revealed specific contamination patterns from the sources of organic matter to predators. The trophic levels involved in the sedimentary benthic food web (S-BFW - based on the sedimentary organic matter) and to a lesser extent in the reef benthic food web (R-BFW - based on algal turf) were mainly contaminated by trace elements that originate from mining activities: Ni and associated trace elements (Co, Cr, Fe, and Mn) were preferentially integrated into these trophic structures. Trace elements linked to agro-industrial (As, Hg, and Zn) and urban (Ag, Cd, Cu, Pb, Se, and V) activities were also integrated into the S-BFW, but preferentially into the R-BFW, and to a lesser extent into the detrital benthic food web (D-BFW) supplied by sea-grass plants. Most of the trace elements were biodiminished with increasing trophic levels along trophic networks. However, a marked biomagnification was observed for Hg, and suspected for Se and Zn. These results provide important baseline information to better interpret trace element contamination in the different organisms and trophic levels in a highly diversified coral reef lagoon.