The Palaeocene–Eocene Thermal Maximum (PETM) interval at the Wadi Nukhul section (Sinai, Egypt) is represented by a 10 cm thick condensed clay-rich layer corresponding to the NP9a–NP9b nannofossil subzone boundary. The Wadi Nukhul Palaeocene–Eocene boundary (PEB) is characterized by (1) an abrupt negative excursion in carbonate and organic carbon isotope ratios (−6‰ in δ13Ccarb and −2‰ δ13Corg), (2) an abrupt persistent negative shift in organic nitrogen isotope values (δ15Norg), (3) a significant increase in phosphorus concentrations just above the carbon isotope excursion, (4) a decrease in carbonate content and significant increase in kaolinite and (5) high vanadium and low manganese contents coincident with the occurrence of framboidal pyrite. The abrupt correlative isotopic excursions of δ13Ccarb, δ13Corg and δ15N suggest that the lowermost part of the PETM is missing. The decrease in carbonate content indicates dilution by high detrital input triggered by acid weathering and carbonate dissolution in response to increased atmospheric CO2 resulting from the oxidation of methane. The sudden increase in kaolinite content reflects a short-lived change to humid conditions. The δ15N values close to 0‰ above the PEB suggest a bloom of N2-fixing cyanobacteria. Increased bacterial activity may be either the cause or the result of the anoxia locally associated with the PETM.