Studies of water masses present in the Channel of Sicily are relevant to understanding not only the overall Mediterranean circulation but also the Tunisian coastal shelf circulation. This study attempts to clarify the dynamics of water masses exchanged through the channel and its variability using data collected during six hydrographic cruises in the western half of the Cap Bon – Mazara del Vallo section during 2003. Hydrographic measurements clearly show the signature of the Atlantic Tunisian Current along the Tunisian coast characterized by important mesoscale variability. Computation of a normalized temperature and salinity standard deviation makes it possible to distinguish areas of high temporal variability located in the transitional layer between the Atlantic Water and the Levantine Intermediate Water. This transitional layer is created by the presence of both Western Intermediate Water and Ionian Water. In addition to highlighting the relevance of the mesoscale activity, a comparison between direct current measurements and adjusted geostrophic currents produced a more confident estimate of the surface and deep transports through the western part of the channel. Our conclusions on seasonal and mesoscale variability are confirmed by a high resolution numerical simulation.