An ecosystem model based on nitrogen cycling and oxygen has been developed for the Thau lagoon. It takes into account the specific features of this Mediterranean lagoon, a semi-confined system with watershed inputs and oyster farming. The ecosystem model uses currents calculated by a two-dimensional hydrodynamic model and integrated into a box model. This model is compared with a year survey data and used to estimate nitrogen and oxygen fluxes between the different ecosystem compartments. The yearly simulation shows that the ecosystem behavior is driven by meteorological forcing, especially rain which causes watershed inputs. These inputs trigger microphytoplankton growth, which is responsible for new primary production. During dry periods, nitrogen is recycled into the lagoon thanks to oysters excretion, sediment release, microzooplankton excretion and mineralization. Ammonium produced in this way is consumed by a population of pico- and nanophytoplankton causing regenerated primary production. Consequently, the ecosystem remains highly productive in summer even without external inputs. Shellfish farming also plays an important role in the whole lagoon through biodeposition. Driven by biodeposition, sediment release is the major source of nitrogen in the water column and causes oxygen reduction. The oysters contribute to the recycling activity by excretion, which supports the regenerated primary production. They are also involved in oxygen consumption by respiration which can cause local hypoxia. Further improvements are proposed before this model may become a functional environmental model for a lagoon ecosystem.