A new 44 kyr long record of dinoflagellate (phytoplanktonic organisms) cysts (dinocysts) is presented from a marine sediment core collected on the Congolese margin with the aim of reconstructing past hydrological changes in the equatorial eastern Atlantic Ocean since Marine Isotopic Stage (MIS) 3. Our high-resolution dinocyst record indicates that significant temperature and moisture variations occurred across the glacial period, the last deglaciation and the Holocene. The use of specific dinocyst taxa, indicative of fluvial, upwelling and Benguela Current past environments for instance, provides insights into the main forcing mechanisms controlling palaeohydrological changes on orbital timescales. In particular, we are able, for the last 44 kyr, to correlate fluvial-sensitive taxa to monsoonal mechanisms related to precession minima–obliquity maxima combinations. While upwelling mechanisms appear as the main drivers for dinoflagellate productivity during MIS 2, dissolved nutrient-enriched Congo River inputs to the ocean also played a significant role in promoting dinoflagellate productivity between approximately 15.5 and 5 ka BP. Finally, this high-resolution dinocyst study permits us to precisely investigate the suborbital timing of the last glacial–interglacial termination, including an atypical warm and wet oceanic LGM signature, northern high-latitude abrupt climate change impacts in the equatorial eastern Atlantic, as well as a two-step decrease in moisture conditions during the Holocene at around 7–6 and 4–3.5 ka BP.