The Lesina lagoon (southern Adriatic Sea, Mediterranean) is a coastal lagoon located in a highly intensified farming and tourist area. A monthly sampling was carried out in 1998 in five stations, representative of different hydrological features, in order to analyse phytoplankton composition and its relation to environmental parameters. Our results showed high spatial variability of abiotic variables. Phytoplankton abundances and biomass trends showed marked seasonality, with annual peaks occurring in late winter-early spring and summer periods. Phytoplankton blooms were due to the diatom Thalassiosira pseudonana and the dinoflagellate Prorocentrum cordatum. Statistical analyses showed that salinity and nutrients were the main factors affecting phytoplankton abundance and biomass. Phytoplankton dynamics was associated both to seasonality and the hydrodynamic regime of the system. Moreover, chemical-physical data were analysed together with those collected in the same stations in 2007, to compare their dynamics under different hydrological regimes. The two periods corresponded to the closure and opening, respectively, of canals connecting the lagoon to the sea. In general, abiotic variables (salinity, dissolved oxygen, pH, nitrate, phosphate and silicate concentrations) were significantly affected by the hydrodynamic regime. These data could provide a useful basis to complement the knowledge gained through current monitoring within the framework of the European Directives, as well as to implement conservation and management strategies of these transitional waters.