Pluriannual data on the phytoplankton spatial and seasonal distribution in the lagoon of Venice (North-western Adriatic Sea, Italy) were presented and analysed to suggest a possible tool for the transitional ecosystem water quality assessment. In order to meet the European Water Framework Directive 2000/60, data of phytoplankton distribution were processed together with environmental parameters to verify whether such a community may give indications of the water quality. Some evidence in this direction appeared to be provided by diatom biomass and cell abundance. The starting hypothesis was that the occurrence of opportunistic species (small cells with a high growth rate) is related to the worst environmental conditions, and the conservative species (large cells with a slow growth rate) to the best water quality areas. The method was validated in other Italian transitional systems (Sacca di Goro, Lesina Lagoon, Orbetello Lagoon, Marano-Grado Lagoon, Mar Piccolo of Taranto). The overall results seem to give quite a good description of the environmental status, but they also highlighted the limits of the phytoplankton community as an indicator and, hence, the necessity to conduct regular sampling throughout the year.