A three-dimensional model coupling physical and biological processes for the whole Than lagoon (Mediterranean coast of France) was developed in order to assess the relationships between macrophytes and the oxygen and nitrogen cycles. Ten species have been inserted as forcing variables in the model. Plankton dynamics, shellfish cultivation impact and mineralization of organic matter are also considered, as well as nutrient and oxygen exchanges between the sediment and the water column. Simulations with and without the macrophytes have shown that the system can be characterized as having a highly structured pattern involving lagoon nitrogen and oxygen cycles. This pattern is created by the combined influence of macrophytes, watershed and oyster farming. The model has been also used to assess the total annual macrophyte production at the whole lagoon scale. Comparisons with phytoplankton production and with results from other temperate lagoons have underlined the high productivity of the Than lagoon supported by active nutrient regeneration. (C) 2003 Elsevier Ltd. All rights reserved.