Dinoflagellate cysts and other palynomorphs were studied from ODP Hole 1002C in the Cariaco Basin over the past 30 000 years. The assemblage shifts between a dominance of heterotrophic dinoflagellate cysts (mainly Brigantedinium spp., Lejeunecysta spp., Selenopemphix nephroides and Stelladinium reidii) and autotrophic dinoflagellate cysts (mainly Spiniferites ramosus, Lingulodinium machaerophorum and Operculodinium centrocarpum). These assemblage shifts are associated with stronger upwelling during stadials and stronger river influx during interstadials. Increases in productivity caused by enhanced upwelling are coupled to improved preservation and vice versa. More stratified water is indicated by higher abundances of L. machaerophorum and succeeds Heinrich events. The average process length of L. machaerophorum can be used to track changes in salinity, since this shows a similar pattern as the δ18OSW (paired Mg/Ca −δ18O) reconstruction. During the last glacial, conditions were more saline than during the current interglacial. On a millennial scale, changes in salinity are opposite to open ocean salinities and the hydrological proxies, which can be explained by a modulation of the signal by stratification, isolation of the Basin or advection of freshwater masses. These results highlight both generalities and particularities of the palaeoecological record of this tropical semi-enclosed basin.