The GAMELag box-model tool is used in a collaborative approach between scientists and ecosystem managers to determine admissible nutrient load in lagoon environments. This case study of its application in a hypereutrophic French Mediterranean lagoon demonstrated its ability to determine exogenous nutrient flows compatible with good ecological status. A new method, based on the exploratory analysis of simulated scenarios of flow reduction (exogenous and endogenous), revealed the predominant role of sediment stocks and exchanges in the ecological status of this lagoon. Reducing inflows from the catchment area allowed sediment release and initiated the restoration of this compartment. A reduction in exogenous nitrogen inputs by a factor of 0.24 and phosphorus by 0.1 was found to be necessary to achieve EU Water Framework Directive objectives. These results are helping lagoon managers to raise the awareness of local stakeholders and co-construct management measures to encourage a dynamic of restoration.