The Salento lagoons site comprises two coastal brackish lagoons located in the South Apulia (SE Italy): Acquatina and Alimini. Acquatina is a semi-artificial and meso-oligotrophic basin with a surface area of 0.45 km2 and an average depth of 1.2 m. Since 1985 the basin has been managed by University of Salento and is the focus of several scientific studies. Alimini is a mesotrophic, relatively small (surface area=1.375 km2) and shallow (average depth=1.5 m) lagoon. In Acquatina, the seagrass Cymodocea nodosa covers more than 50% of the lagoon bottoms, while other seagrasses of the genus Ruppia and Zostera together with macroalgae of the genera Ulva, Ceranium, Chondria and Caulerpa are locally abundant. In Alimini lagoon, primary producers are restricted to phytoplankton (Thalassiosira sp.; Chaetoceros sp. ) and submerged macrophytes (Phragmites australis). Dominant benthic species are Heteromastus filiformis, Cirrophorus furcatus, Cerithium vulgatum and Loripes lacteus in Acquatina, while Loripes lacteus, Heteromastus filiformis and Owenia fusiformis in Alimini. Mullets, eels, sea-bass and sea-bream are the main fish species present in both ecosystems. Acquatina and Alimini lagoons are relatively pristine ecosystems. A small human impact is mainly related to the discharge of nutrients into the lagoons due to inland agricultural activities and fishing activities. Both ecosystems are included in Natura 2000 sites according to the Habitats Directive.