Analysis of morphological, geological and environmental characteristics of the Fusaro Lagoon has shown the present degraded condition of the lagoon and the perilagoon area. The lagoon developed during the mid-Holocene within a wide marine bay confined between the coastal volcanic structures of Mt. Cuma to the north and Torregaveta to the south in the western part of the Phlegrean Fields. Subsequently, the bay was gradually filled with pyroclastic materials from phlegrean eruptive vents and sediments carried by the rivers Volturno and Clanis, thus, creating an open lagoon. It then evolved into a partially closed lagoon due to the formation of a continuous littoral spit during the late Holocene, probably wider than the present-day one and surrounded by marshlands. Finally, the total closure of the lagoon took place in the Graeco-Roman period, following the stabilization of the dune ridge, and it assumed a shape similar to present-day one only towards the end of the 18th century. Between the Roman period and 1941, three lagoon channels were opened in order to avoid the frequent environmental crises which continue to affect, although for different reasons, this salt-water basin. The basin has been exploited for more than 2000 years not only for mollusc culture and pisciculture, but also for the maceration of hemp and flax. In the 1980s, in order to reduce the effects of the environmental crises, dredging of the lagoon bottom has been carried out, altering the hydrogeological equilibrium and that of the ecosystem. Over the past 30 years, the supply of raw sewage of domestic, agricultural and industrial origin has ensured the presence of a high concentration of pollutants, including heavy metals. On the basis of the data obtained and in order to restore this sensitive transitional environment, eco-compatible interventions are proposed which aim at morphological and hydrologic resettlement, abatement of pollutants on the bottom of the basin, reintroduction of endemic molluscs, together with monitoring the quality of sediments and both sea-lagoon waters and groundwater.