Gebel Nezzi (Upper Nile Valley, Egypt) was chosen to study the middle Palaeocene planktonic foraminiferans, nannoplankton contents, benthic foraminiferans, and stable isotopes to provide additional information into sea‐level changes. Two negative excursions are recorded that are associated with a sharp change in palaeoenvironmental conditions, representing significant global palaeoceanographic, palaeoclimatic, and eustatic events observed at other sites around the world. They are characterized by a drop in total foraminiferal abundance associated with a drop in the type, species richness, frequency, and diversity of foraminifers. The first negative excursion of −0.6‰ δ13C and −0.5 δ18O occurs during the Late Danian Event (LDE) almost near the upper part of the planktonic foraminiferal P3a Subzone and within the calcareous nannofossil NTp8A Subzone at the top of the lower third of Chron C26r. It is dominated by shallow‐water benthic foraminiferans of the Neoeponides duwi biofacies. The Danian‐Selandian boundary lies directly above the LDE within the top of the nannofossil Zone NP4, and within the planktonic foraminiferal Subzone P3b with significant increases in angular morozovellids associated with the earliest Cenozoic hyperthermals. The second negative excursion of −0.6‰ δ13C and −2.2 δ18O occurs near the top of the Dakhla Formation and is dominated by the benthic foraminiferal Bulimina farafraensis biofacies within the upper part of the calcareous nannofossil NTp9 Subzone and upper part of the planktonic foraminiferal P4a Subzone. These negative excursions associated with a well‐known falling sea level and are an important tool for regional correlation. Fluctuations in the foraminiferal population, benthic biofacies, δ 13C and δ18O isotopes and carbonate content reflect three fourth‐order transgressive–regressive (T–R) sequences response to eustatic changes in the Egyptian stable tectonic shelf.