The dramatic global extinction of 35%–50% of benthic foraminifera species in the deep sea in the latest Paleocene and associated negative excursions in δ13C and δ18O may be related to spreading of warm, saline bottom water from subtropical Tethyan shallow regions over the sea floor worldwide. Our study of neritic sections in Egypt shows that in the southern shallow Tethys, a prominent long-term change in bottom-water chemistry, sedimentation, and benthic foraminifera fauna was initiated at the time when the deep-sea benthic extinction event (BEE) took place. Bottom-water δ13C values on the Tethyan shelf show a sudden 3.0‰ negative shift at this event; however, contrary to the deep sea, in which the δ13C excursion was of short duration, Tethyan δ13C values did not fully return to preboundary values, but remained depressed by ∼1.5‰ for at least 1 m.y. The δ13C values at the Egyptian shelf during the BEE are much lower than would be expected if this was a source region for global deep water. The δ18O values indicate no significant change in bottom-water salinity or temperature at the BEE. The long-lasting environmental changes that began on the Egyptian shelf at the BEE may be related to, for example, gateway reorganization along the Tethyan seaway. Paleogeographic changes possibly also triggered a change in the loci of global deep-water formation; however, these loci must be sought in another part of the Tethys.