In order to assess the effects of palaeoenvironmental fluctuations on the distributions of calcareous nannofossils and foraminifer species, semiquantitative analyses were carried out on a cored upper Aptian section in the Sergipe Basin, northeastern Brazil. In the lower part of the section, abundance peaks of Watznaueria barnesae, Nannoconus spp., and favusellids (a planktic foraminiferal morphogroup adapted to shallow, warm, carbonate-saturated environments) document the earliest marine incursions in northeastern Brazil and appear to represent cyclic short-term marine pulses in an environmental setting dominated by paralic conditions. Higher in the succession, where open marine, shallow–middle neritic conditions became well established, a negative correlation is seen between the abundance of Nannoconus spp. and coccoliths (Tranolithus spp., Stradneria spp. and W. barnesae) as nutrient levels fluctuated. Tranolithus spp. and Stradneria spp. are probable indicators of nutrient enrichment in very shallow-water environments, associated with the onset of marine transgressive events. A positive correlation between nannoconids, favusellids, and carbonate-rich deposits, indicates that both fossil groups thrived in the same environmental conditions (shallow, warm, hypersaline, carbonate-saturated environments with intermediate, mesotrophic, nutrient levels).