New dinoflagellate cyst (dinocyst) analyses were carried out at high-resolution in core MD99-2339, retrieved from a contouritic field in the central part of the Gulf of Cadiz, for the Marine Isotope Stage (MIS) 3 interval, allowing to discuss paleohydrological changes over the last 50 ky in the subtropical NE Atlantic Ocean. Some index dinocyst taxa, according to their (paleo) ecological significance, shed light on significant sea-surface changes. Superimposed on the general decreasing pattern of dinocyst export to the seafloor over the last 50 ky, paralleling the general context of decreasing aeolian dust fertilization, a complex variability in dinocyst assemblages was detected at millennial timescale. Enhanced fluvial discharges occurred during Greenland Interstadials (GI) and especially GI 1, 8 and 12, while enhanced upwelling cell dynamics were suggested during the Last Glacial Maximum and Heinrich Stadials. Finally, during the early Holocene, and more specifically during the Sapropel 1 interval (around 7–9 ka BP), we evidenced a strong decrease in dinocyst fluxes, which occurred synchronously to a strong reduction in Mediterranean Outflow Water strength, and that we attributed to an advection of warm and nutrient-poor subtropical North Atlantic Central Waters. Over the last 50 ky, our study thus allows capturing and documenting the fine tuning existing between terrestrial and marine realms in North Atlantic subtropical latitudes, not only in response to the regional climate pattern, but also to monsoonal forcing interfering during precession-driven northern hemisphere insolation maxima. This mechanism, well expressed during the Holocene, is superimposed on the pervasive role of the obliquity as a first major trigger for explaining migration of dinocyst productive centres in the NE Atlantic margin to the subtropical (temperate) latitudes during glacial (interglacial) periods.