The major part of the New Caledonia (NC) lagoon was classified as UNESCO Natural Site of Humanity Patrimony. Indeed, 22 175 km(2) of tropical coral lagoon area exhibit high biodiversity. The NC lagoon is semi enclosed and connected to the Coral Sea through a barrier reef segmented by narrow passes. The environment is oligotrophic, due to important flush during trade winds events, and bathymetry is highly variable. In order to predict eutrophication events, we used an extension of a 3D coupled physical-biogeochemical model recently developed on NC south western lagoon. The model is based on the Nitrogen and Carbon cycles, relating the variable stoechiometry of the elements in each biological compartment. The ecological model was developed to include an explicit description of the microbial loop. The resulting coupled model, forced by tide, wind, light, temperature and freshwater inputs, was used to calculate phytoplankton biomass, bacterial production, dissolved organic matter concentrations and nutrient recycling. Here we present results issued from the 3D coupled model ECO3M_LAGOON (biogeochemical, LOPB-IRD) and MARS3D (regional physical model, IFREMER-IRD) describing spatial and temporal interactions between water motion and biology, on larger domain including reef barrier and water exchanges through ocean-lagoon interface. To validate physical processes in the lagoon we used in situ data collected during field cruise (ValHyBio 2008, La Nina episode). Surface chlorophyll concentrations are compared with water color data from ValHyBio cruise and satellite date (MODIS/MERIS) corrected from bathymetry effects.