The Pliocene–Pleistocene sequences in the Nile Delta are of immense economic significance due to their hydrocarbon potential. Hence, a better understanding of the time-calibrated basinal palaeoenvironmental changes is essential to improve the hydrocarbon recovery. A total of 182 sub-surface samples from the Sapphire-DC well in the offshore north-western part of the Nile Delta were analysed to reveal changes in calcareous nannofossil assemblage composition and palaeoenvironments during the late Miocene–Pleistocene (5.44–0.43 Ma). Sixteen marker bioevents and nine biozones are identified for the first time. The absence of Ceratolithus acutus suggests a hiatus at the Messinian–Zanclean (Miocene–Pliocene) boundary. The studied interval is marked by the dominance of five species; Pseudoemiliania lacunosa (24%), small Gephyrocapsa sp. (20%), Helicosphaera kamptneri (11%), Reticulofenestra minutula (10%) and Calcidiscus leptoporus (6%). Based on their distribution patterns, six intervals (Intervals 0 to 5) are identified. Throughout the study interval, cooler waters (except during Interval 0; Messinian Salinity Crisis, MSC, 5.44–5.26 Ma) and eutrophic conditions persisted within a shallow hemipelagic and near-continental setting, marked by moderate-to-high terrigenous input (more for Intervals 4 and 5; ˜2.73–0.42). Additionally, low species diversity and high species dominance are identified, suggesting a stressed environment. Species diversity shows a gradually declining trend, up section, whereas species dominance correspondingly increases. Interval 0 (MSC) is dominated by warm water species of Sphenolithus abies and Helicosphaera kamptneri. The cool water species, Reticulofenestra pseudoumbilica, and small Gephyrocapsa dominate in Interval 1; small Gephyrocapsa dominates in Interval 2. Interval 3 is marked by the deepening of the basin with a brief introduction of warm, somewhat oligotrophic and open-ocean waters. In the middle of this interval (at 3.73 Ma; the Early–Late Pliocene boundary), an abrupt decrease in species diversity with a corresponding increase in species dominance suggests deteriorating conditions. Interval 3 also encompasses the mid–late Pliocene warming period, which in the Nile Delta is marked by cooler waters. Intervals 3–5 are dominated by P. lacunosa, suggesting a continuation of cool waters and eutrophic conditions. Hence, throughout the study interval, cooler waters (except during the MSC) and eutrophic conditions within in a shallow hemipelagic and near-continental setting are inferred with moderate-to-high terrigenous input and low species diversity and higher species dominance, suggestive of stressed environmental conditions.