The Cretaceous–Paleogene (K–Pg) boundary interval at Gabal Aras, Qena region (part of the southern Tethyan margin) was investigated in detail for calcareous nannofossil and foraminiferal (planktonic and benthonic) assemblages to characterize the surface and bottom sea water conditions. The K–Pg boundary is marked by a minor hiatus expressed by the absence of the lowermost Danian P0 and Pα planktonic foraminiferal zones. Benthonic foraminifera assemblages indicate moderately oxygenated bottom sea waters associated with oligo-mesotrophic conditions during early late Maastrichtian, and mesotrophic conditions during the latest Maastrichtian. The benthonic foraminiferal assemblage reflects a decrease in the food supply in the bottom sea water during the early Danian, while well-oxygenated and oligotrophic conditions dominated during late Danian. The late Maastrichtian surface water witnessed a general cooling trend that was interrupted by a warming episode that could correspond to the Late Maastrichtian Warming Event (LMWE). Acme of Thoracosphaera associated with increased abundance of Neobiscutum romeinii were observed within the upper part of NP1 Zone indicating stressful surface water conditions. The increase of the epifaunal foraminiferal taxa and the occurrence of Cruciplacolithus primus throughout NP2 and NP3 zones reflect a progressive return to normal marine conditions. In the framework of sequence stratigraphy, two third-order depositional sequences covering the K–Pg boundary interval were identified, interpreted, and correlated. The obtained sea-level curve was evaluated to assess whether it was controlled by the eustatic sea-level changes, regional tectonics, or both these factors.