The Biguglia lagoon, located in the northwestern Mediterranean Sea (Corsica), is a natural reserve, which has been affected by a tremendous territorial change since last decades. An ecosystem-based approach should enable to understand the functioning of an ecosystem, which can be considered, as a socio-ecosystem in order to provide decision support for its conservation and restoration. The objective of this work is to present the research approach carried out on the Biguglia lagoon. The decreasing of the water quality is reflected by a shift from a dominance of aquatic magnoliophytes in the 1970s to varying dominance of phytoplankton and opportunistic macroalgae in the early 2000s. At the same time, it has been observed an ongoing deterioration of the quality of groundwater partly providing the lagoon with fresh water, which can be attributed to the uncontrolled urbanization development all over the alluvial plain surrounding the lagoon. Efforts undertaken to improve the hydraulic management and the reduction of nutrient inputs in the watershed allowed to observe signs of ecological restoration. Nevertheless, the socio-ecosystem functioning study requires a multidisciplinary approach where the natural and social scientists must work together as it is conducted within the framework of the Human-Environment Observatory of the Mediterranean coast (OHM-LM).