The management of coastal lagoons is of particular interest due to their high economical importance. In spite of their great productivity, coastal lagoons are often impacted by human pressure which produces water eutrophication. The aim of this paper is to assess the trophic state of the two Mediterranean lagoons taking into account chemical-physical parameters, nutrient concentrations and biological parameters. Two Italian lagoons, Orbetello and Varano (respectively located in Tyrrhenian and Adriatic coast, Italy) were studied between May 2003 and April 2005. Both these systems receive treated urban outflows, agricultural effluents and rivers freshwater inputs. Field collected data showed that studied lagoons were characterized by different human and natural pressures. Orbetello showed the highest water eutrophication, highlighted by the trophic index values, while Varano showed lower eutrophication levels except for the summertime. The values of physical, chemical and biological parameters measured in Orbetello and Varano lagoons indicate that a wide spatial and seasonal gradient of the water characteristics was established during the study period, but in particular in winter. This gradient, typical of estuarine systems, was essentially due to the mixing of freshwater, seawater and anthropogenic inputs. Orbetello lagoon seemed much more affected by the urban impact and the fish-farming activities than Varano lagoon, but the latter showed a greater agriculture activities impact as showed by the remote sensing images.