Mangroves of New Caledonia act as a buffer between a lagoon of more than 20,000 km2 and the Island, which suffers intense processes of erosion resulting from urbanization and natural resources exploitation. This preliminary study aims at determining how heavy metals are distributed in mangrove sediments and pore-waters in relationship with their organic content. To reach our goal, a series of 50-cm deep cores were collected in the mangrove of Conception Bay. The various coring sites are representative of live forests (Avicennia marina, Rhizophora stylosa), dead forest, and intertidal unvegetated area. The ranges of concentrations in sediments were the following (μmol g−1): Cu (0.08 to 0.51), Co (0.01 to 0.38), Ni (0.03 to 3.55), Cr (0.36 to 3.11), Zn (0.68 to 2.36), Mn (1.13 to 5.0) and Fe (22.64 to 721.69). Heavy metals distribution within sediments and pore-water appear to result from diagenetic processes linked to OM decomposition. Beneath the dead Avicennia forest and in the unvegetated sediments, the higher the organic content, the higher the metal concentration in the solid phase. Beneath living mangrove stands, despite a higher organic content, as well as higher sulphur content, heavy metals concentrations were not higher than those measured in the other sampling sites. Beneath these forests, redox conditions were mainly controlled by the length of waterlogging and the activity of root system. We suggest that, because of the specificity of the Avicennia root system and its position in the intertidal zone, heavy metals are more bioavailable and potentially more mobile than beneath Rhizophora stand.