Fourteen trace elements (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, V, and Zn) were analyzed in livers and muscles from 22 fish species from the New Caledonia lagoon, which is subjected to important chemical inputs due to intense land-based mining activities (New Caledonia is the third largest world producer of Ni). The results of this baseline research indicated that livers generally concentrated trace elements to a greater extent than muscles. Nevertheless, the overall trace element concentrations in both tissues were barely above the levels reported in fish and thus contamination at the local scale was poorly discriminated. Although these levels were low, preliminary risk assessment from a global health standpoints suggest that As could potentially lead to concern for fish consumers. Based on the trace element concentrations in livers and the fish trophic preferences, some tendencies have been observed among trophic groups: Ag, Cu, Fe, Hg, and Zn concentrations were generally higher in liver of fish with the highest trophic position whereas Cd concentrations were lower in these groups. The use of the leopard coral grouper Plectropomus leopardus as a resident top predator allowed determining the geographical variations in contamination levels with significant differences in six out of the fourteen elements investigated. The sampling sites influenced by anthropogenic inputs were revealed by high Ag, Cd, Cu, Hg, and Pb concentrations. Such geographic differences also applied to Zn but surprisingly not for the typical elements associated with Ni mining, i.e., Co, Cr, Mn and Ni.