||Coral reef lagoons are under the growing influence of anthropogenic activities, leading to increasing loads of nutrients and various contaminants. Modelling approaches are a useful tool for studying such a complex coastal environment. In this study, we carried out the development of a three-dimensional coupled hydrodynamical-biogeochemical model of the south-west lagoon of New Caledonia. The biogeochemical model presented in Faure et al. (2006, 2010) was dynamically coupled with a hydrodynamical model (MARS3D) in order to study the short-term variability of the ecosystem. Two simulations (in winter and summer) were then performed from measured initial conditions using realistic wind and irradiance conditions and river inputs. Examinations of the biogeochemical response to these transient meteorological conditions were presented and compared with temporal field data corresponding to the considered periods. Results highlighted the ecosystem functioning, based on the balance of hydrodynamical and biogeochemical processes. Influence of urban and terrigeneous inputs were limited to the coastal zone. The model accurately reproduced the measured Chl.a and bacterial production, highlighting the improvement made on the biogeochemical model. However, the underestimation of some variables in model outputs, in particular nutrients, led us to focus on different inputs, such as sediment inputs which were not taken into account or properly estimated. Moreover, the role of boundary waters appeared crucial and suggested a calibration effort. Last, the final aim of our modelling study will help the development of a useful tool for studying the key processes of the ecosystem of the south-west lagoon of New Caledonia, as well as the examination of the biogeochemical response under different scenarios.