Coral reef lagoons of New Caledonia form the second longest barrier reef in the world. The island of New Caledonia is also one of the main producers of nickel (Ni) worldwide. Therefore, understanding the fate of metals in its lagoon waters generated from mining production is essential to improving the management of the mining activities and to preserve the ecosystems. In this paper, the vertical fluxes of suspended particulate matter (SPM) and metals were quantified in three bays during a dry season. The vertical particulate flux (on average 37.70 ± 14.60 g·m 2 ·d −1) showed fractions rich in fine particles. In Boulari Bay (moderately impacted by the mining activities), fluxes were mostly influenced by winds and SPM loads. In the highly impacted bay of St Vincent and in the weakly impacted bay of Dumbéa, tide cycles clearly constrained the SPM and metal dynamics. Metals were associated with clay and iron minerals transported by rivers and lagoonal minerals, such as carbonates, and possibly neoformed clay as suggested by an unusually Ni-rich serpentine. Particle aggregation phenomena led to a reduction in the metal concentrations in the SPM, as identified by the decline in the metal distribution constants (K d).