The Augusta basin, located in SE Sicily (southern Italy), is a semi-enclosed marine area, labelled as a highly contaminated site. The release of mercury into the harbour seawater and its dispersion to the blue water, make the Augusta basin a potential source of anthropogenic pollution for the Mediterranean Sea. A mass balance was implemented to calculate the HgT budget in the Augusta basin. Results suggest that an average of ∼0.073 kmol of HgT is released, by diffusion, on a yearly basis, from sediments to the seawater, with a consequent output of 0.162 kmol y(-1) to coastal and offshore waters; this makes the Augusta area an important contributor of mercury to the Mediterranean Sea. Owing to the geographical location of the Augusta basin, its outflowing shelf-waters are immediately intercepted by the surface Atlantic Ionian Stream (AIS) and mixed with the main gyres of the eastern Mediterranean Sea, thus representing a risk for the large-scale marine system.