The Mar Menor lagoon is one of the largest coastal lagoons (135 km2 surface) of the Mediterranean basin. It receives runoff waters coming from the nearby intensive agricultural area of Campo de Cartagena, which have led this lagoon to be declared as a sensitive area for eutrophication in June 2001 under European Directive 91/271/EEC and as a vulnerable zone for nitrates contamination in December 2002 under Directive 91/676/EEC. Moreover, the existence of mining activities (nowadays discontinued) in the nearby area of Sierra de Cartagena-La Union has caused the spread of metal polluted wastes into the Mar Menor lagoon and its salt marshes. As a consequence, huge coastal areas are buried by metal enriched wastes, and although most of them have been colonized by vegetation, others remain bare and exposed to erosive agents (e.g. wind, water). At the same time, the Mar Menor and its salt marshes have been included in the Ramsar Convention on Wetlands. Also, it is a Special Protected Area of Mediterranean Interest (SPAMI), a Specially Protected Area (SPA) under the EU Wild Birds Directive and a Site of Community Importance (SCI) to be integrated in the Nature 2000 Network (EU Habitats Directive). In addition, the Campo de Cartagena- Mar Menor zone hosts important economic activities related with agriculture, fisheries and tourism (Conesa and Jiménez-Cárceles, 2007). Hence, the habitat conservation and the uses of the territory must be compatible and overcome the environmental problems of the zone.