The Berre Lagoon is one of the biggest Mediterranean lagoons. It receives freshwater from two anthropised rivers and from a hydroelectric powerplant. As a consequence, high variations of salinity and eutrophication prevent the establishment of a balanced ecosystem. The TELEMAC© 3D model was used to simulate hydrodynamics, salinity and temperature. Then it was coupled to the water quality model DELWAQ© to simulate the biogeochemical cycles. Both models were parameterized and validated thanks to an important data base fed with a continuous real-time monitoring at several stations. This models coupling is the only way to compile the physical and biogeochemical variables and processes. It’s a tool aiming at a better assessment of the high complexity of the lagoon nutrients cycles. We would be able to test various managing scenarios and to suggest new rehabilitation strategies.