This study presents novel findings on the drivers of the calcitic planktonic foraminiferal and aragonitic pteropod Holocene assemblages of the North Aegean Trough (northeastern Mediterranean), an area recording the interaction between dynamic water masses as they exchange between the northern and southern Mediterranean sub-basins. Both of these groups of microorganisms are the major producers of calcium carbonate in the ocean, and are particularly sensitive to climate and oceanographic changes over the late Quaternary. Downcore micropaleontological data from the gravity core AEX-15, supplemented with multivariate statistical Q-mode cluster and principal component analyses (PCA) results, provide significant insights on the water column dynamics during the Holocene. Focusing on the last ~10 calibrated thousands of years before the present day (ka cal BP), our integrated study reveals that primary productivity is the dominant factor controlling the planktonic foraminifera distribution in the North Aegean Sea, whereas water column stratification, and particularly the intensity of the oxygen minimum zone, seems to be the major driver on the pteropod distribution. Besides productivity and thermal stratification, which show the highest explanatory power for planktonic foraminifera and pteropod communities, respectively, though they affect both groups to a different extent, upwelling seems to further affect both faunal groups. Overall, our findings are consistent with those derived by published late Quaternary eastern Mediterranean records, highlighting in parallel a useful additional dimension on planktonic foraminiferal and pteropod ecology, which is inextricably linked with the factors of primary productivity and vertical stratification of the warm Holocene water column.