The Strait of Otranto is a 75-km-wide and ˜300-m-deep (on average) inlet that separates the Adriatic and Ionian Seas (Figure 1). It is the southern open boundary of the Adriatic Sea, which is a semi-enclosed, shallow basin. The forcing through this open boundary plays an important role in driving the general circulation of the Adriatic, which, in turn, affects the biochemical properties in the two adjacent basins. The Strait of Otranto is also a key area for the entire Eastern Mediterranean deep circulation, since the Adriatic Sea presumably produces most of the Mediterranean's bottom water. The monitoring of water mass transport in the strait and the study of the water exchange dynamics are therefore crucial for an understanding of a broad range of oceanographic processes in the Adriatic and in the entire Eastern Mediterranean, as well as for addressing environmental issues, such as pollution that spreads from coastal to deep-sea areas.