Aiming at portraying the Aegean's water mass structure and identifying Dense Water Formation processes, two winter cruises were conducted in 2005–2006, across the plateaus and depressions of the Aegean Sea. The most prominent feature of the water mass distribution in the basin is a distinct “X-shape” of the Θ-S characteristics, suggesting a complicated coupling of the major Aegean sub-basins. The surface and deep waters are relatively decoupled with diverse origin characteristics, while the intermediate layers act as connectors of the main thermohaline cells. The Central Aegean seems to play a key role due to formation processes of water masses with densities equal and/or higher than 29.2 kg/m3, that take place in the sub-basin and disperses in the North Aegean. On the other hand, the South Aegean appears greatly influenced by the Eastern Mediterranean circulation and water mass distribution, especially under the Eastern Mediterranean Transient status. The Transitional Mediterranean Water monitored in the post-EMT period and characterized by low temperature at 14.2°C, low salinity at 38.92 and low dissolved oxygen at 3.97 ml/l, with its core around 750 m and above the saline (39.06) Cretan Deep Water, altered significantly the South Aegean structure. The pre-EMT thermohaline pattern of the Central and South Aegean deep layers were similar, while the bottom density of the Central basin was higher than that in the South Aegean. Thus, it is possible that the deep waters of the Central Aegean acted as a dense water reserve supply for the deeper part of the Southern basin.