Fluorescence, polarographic and potentiometric analysis of sea water from the New Caledonia lagoon (located south of Noumea) allowed the determination of the specific properties of the dissolved and particulate phases of organic matter (OM)-metal complexes according to various regions of the lagoon. In particular, OM complexes with Ni, Zn, Pb, Cu, Cd were chosen in this study due to the sensitivity of these complexes to affect biocenosis of the nearby enclosed coral reef as well as their availability to enter the coast from erosion (terrigenous OM) or human activities from nickel extraction or pollution from waste sites (anthopogenic OM) that exist throughout New Caledonia. Combined with geochemical modelling, the OM-metal complexes analysis allowed the determination of their conditional stability constants which in turn helped in predicting the fate of the metal pollution in the lagoon. For the first time, fluorescence, polarographic and potentiometric techniques combined with geochemical models that employed discrete pKa distribution on OM enabled the determination of the origin of the OM, as either natural or anthopogenic.