Hydrographic conditions in the Mozambique Channel are dominated by the passing of large anticyclonic eddies, propagating poleward into the upstream Agulhas area. Further south, these eddies have been found to control the shedding of Agulhas rings into the Atlantic ocean, thereby playing a key role in Indo-Atlantic Ocean exchange. The element composition of several planktonic foraminifera species collected from sediment trap samples, was compared to in situ water column data from the Mozambique Channel. Single-chamber trace element composition of these foraminifera reveals a close coupling with hydrographic changes induced by anticyclonic eddies. Obtained Mg/Ca values for the surface dwelling Globigerinoides ruber as well as the thermocline dwelling Neogloboquadrina dutertrei follow temperature changes and reduced temperature stratification during eddy conditions. At greater depth, Globorotalia scitula and Pulleniatina obliquiloculata record stable temperatures and thus respond to hydrographic changes with a deepening in habitat depth. Furthermore, test Mn/Ca values indicate a close relationship between water column oxygenation and Mn incorporation in these planktonic foraminiferal species.