The seasonal and interannual variability of the local hydrography in 3 bays (Saros, Izmir, and Gokova bays) along the eastern coast of the Aegean Sea are investigated using data sets collected from 1991 to 2010. The data cover the last major deep-water formation episodes and the Eastern Mediterranean Transient (EMT) relaxation period. Aegean Sea hydrology and water mass characteristics influence the water properties of the bays. The data suggest that Saros Bay (North Aegean Sea), Izmir Bay (Central Aegean Sea), and Gokova Bay (South Aegean Sea) have different physical processes and water characteristics. They have their own dynamics independent from the Aegean Sea. At the same time, they are occasionally influenced by the Aegean Sea's physical processes. The time evolution of water properties inside the bays is investigated by analyzing the temperature, salinity, and density. The bays' data show the relaxation period of the EMT, which continued well into the early 2000s. It is known that this variability depends on the changing climate over the Mediterranean area. Our analysis reveals that the dense water formation in the Central Aegean Sea is considerably connected to the anomalous decrease in winter atmospheric temperature during the EMT period. The isopycnal levels started to increase again and reached their maximum after the EMT relaxation period in the summer of 2007 together with a salinity increase in the water column. The outcropping of isopycnals could have been a sign of a new formation of very dense water in the Aegean Sea.