The bay is a highly fertile Egyptian coastal region but suffers from acute eutrophication and pollution from untreated industrial and domestic waste.

A combination of Islamic texts and investigation using geoarchaeology suggest that this branch was still in existence in the eighth century, when a major inundation caused eastern Canopus to sink into the bay.

[2] Land in the area of Canopus was subject to rising sea levels, earthquakes, tsunamis, and large parts of it seem to have already succumbed to soil liquefaction sometime at the end of the 2nd century BC,[3] becoming submerged.

[4] The eastern part of ancient city of Canopus is submerged in the bay,[5] along with the remains of Menouthis[6] and its sister-city Herakleion–Thonis which now lies 7 kilometres offshore.

In November 2017, the Egyptian mission in cooperation with the European Institute for Underwater Archaeology announced the discovery of 2.000-year-old three sunken shipwrecks dated back to the Roman Era in Alexandria's Abu Qir Bay.

[8][9] The sunken cargo included a royal head of crystal perhaps belong to the commander of the Roman armies of “Antonio”, three gold coins from the era of Emperor Octavius Augustus, large wooden planks and pottery vessels.

[10] In July 2019, a smaller Greek temple and ancient granite columns, treasure-laden ships, along with bronze coins from the reign of Ptolemy II, pottery dating back to the third and fourth centuries BC were found at the sunken city of Heracleion, known as Egypt's Atlantis.

Bad weather delayed disembarkation by a week but, on 8 March, Captain Alexander Cochrane of HMS Ajax deployed 320 boats, in double line abreast, to bring the troops ashore.