Of the three ancient Egyptian (Egypt, ancient) structures on the site, one, the funerary temple of King Mentuhotep II (built c. 1970 BCE), has lost much of its superstructure. The second, the terraced temple of Queen Hatshepsut (built c. 1470 BCE), was uncovered (1894–96) beneath the monastery ruins and subsequently underwent partial restoration. A fuller restoration of the third terrace, sanctuary, and retaining wall was started in 1968 by a Polish archaeological mission, which also found a third temple, built by Thutmose III about 1435 BCE, above and between the two earlier temples. All three temples were linked by long causeways to valley temples with docking facilities. Situated under one of the cliffs, Hatshepsut's temple in particular is a famous example of creative architectural exploitation of a site. All three temples were largely destroyed by progressive rock falls from the cliffs above.

During the Third Intermediate period (Egypt, ancient) (1075–656 BCE) the area of Dayr al-Baḥrī was used as a private cemetery, and in the Ptolemaic period (Egypt, ancient) the sanctuary of Amon in Hatshepsut's temple was refurbished and rededicated to the deified individuals Imhotep and Amenhotep, son of Hapu. The temple of Hatshepsut was the site of a terrorist attack in 1997 in which more than 60 people, many of them tourists, were killed.