Aspects of paleoclimatic and paleoceanographic evolution of the north Aegean Sea through the Holocene are revealed by the study of quantitative variations in planktonic foraminiferal, pteropodal, and palynomorph assemblages; the isotopic composition of planktonic foraminifera; and hydrographic-related indices, extracted from two high-sedimentation rate cores from the North Aegean Trough. Focusing on the last ~10 cal ka BP, the current Holocene subdivision (Greenlandian, Northgrippian, and Meghalayan) confirms the traditional understanding of an evolution from wetter (Greenlandian) to gradually drier (Northgrippian and Meghalayan) climatic conditions and further highlights the role of changing seasonality during this time. The most warm and humid phase corresponds to the time of the sapropel S1 deposition (9.6–6.1 cal ka BP). The Holocene climatic instability of the study area is further supported by six episodes of brief cooling (North Aegean cooling; NAEGC6–NAEGC1) centered at 9.30, 8.05, 7.05, 4.55, 3.55, and 2.05 cal ka BP, reflected by significant faunal changes and oxygen isotope enrichments. These cold/arid events are coeval with equivalent cooling events that have been described in different basins of the Mediterranean Sea, while signal similarities with equivalent changes in the intensity of the Siberian high suggest a climatic link between the studied area and the high-latitude areas.