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Transitional waters represent high valuable wetlands characterized by extremely dynamic processes and irregular temporal trends. These coastal areas are vulnerable interface systems sensitive to natural and human pressures that cause a continuous environmental degradation and a consequential unbalance of the natural ecosystem. Monitoring plays a key role in the management of these ecosystems in order to prevent further deterioration and enhance the status of environmental quality. This paper aims to evaluate the ecological and chemical status of five Sicilian transitional waters systems (Oliveri-Tindari, Cape Peloro, Vendicari, Longarini-Cuba and Marsala) over a 3-year monitoring cycle according to the Water Framework Directive (WFD, 2000/60/EC). The water quality exhibited negative evidences since no water body monitored achieved the overall good environmental status assessed by different biological and chemical elements.