The Ceara Rise lies just beyond the edge of the Amazon River Fan and sediments from this site may record the complex interplay of different climatic systems and processes, including past changes in southern America monsoon activity, Intertropical Convergence Zone setting, different Atlantic Meridional Overturning Circulation (AMOC) strength and phytoplankton blooming triggered by Amazon River plumes. Here we investigate early Pleistocene calcareous nannoplankton at Ceara Rise, between about 1150 and 850 kiloyears ago. Our investigation shows abrupt variations in water column dynamics across glacial/interglacial cycles or, even better, linked with different AMOC modes. Dominant placoliths indicate a shallow nutricline that alternate with dominant Florisphaera profunda, pointing to a deep nutricline, respectively during a vigorous flow and slowdown/shutdown of AMOC. The southward displacement of the ITCZ, higher zonal trade wind intensity, more intense and prolonged North Brazilian Current retroflection and the arrival of the nutrient-depleted Glacial North Atlantic Intermediate Water possibly explain thermocline deepening and increased water column stratification during cold phases, with an Antarctic deep water signature on the Ceara Rise seafloor.