We analysed in situ CTD data collected on 36 joint Tunisian–Italian oceanographic cruises in the Tunisia–Sicily Channel (Cap Bon–Mazara del Vallo section) from 1995 to 2009 in order to identify the water masses in the region and to estimate the interannual variability of their hydrological characteristics. Besides the well-known AW (Atlantic Water) and LIW (Levantine Intermediate Water), other water masses have been identified though their presence is neither as steady nor as stable as the aforementioned ones. The WIW (Western Intermediate Water) flows beneath the AW towards the eastern basin while the IW (Ionian Water), with a highly intermittent character, flows within the subsurface layer towards the western basin. The flow of subsurface water (WIW and IW) is affected by intense mixing which modifies the water masses, tending to make them disappear. Moreover, the same hydrological time series produced interesting results concerning the increase in both temperature and salinity in the Tunisia–Sicily Channel. This trend especially concerns the deeper layers (LIW and tEMDW, i.e. transitional Eastern Mediterranean Deep Water) and we hypothesise that this is a direct response to climatic change occurring in the eastern basin.