Submerged under 150 feet of water, the site sits in what is now the Bay of Aboukir. In the 8th Century BC, when the city is thought to have been built, it would have sat at the mouth of the River Nile delta as it opened up into the Mediterranean.
Scientists still have little idea what caused the city to slip into the water nearly 1,000 years later, but it is thought that gradual sea level rise combined with a sudden collapse of the unstable sediment the city was built on caused the area to drop by around 12 feet.
Over time the city faded from memory and its existence, along with other lost settlements along the coast, was only known from a few ancient texts.
Back in high school I thought that one problem archeologists faced in studying ancient human groups was evidence buried by rising sea levels after the last ice age. In modern times, even with our extensive infrastructure, ways to control our dwelling space's climate, and means of traveling long distances with relative ease, people still primarily live near coasts and rivers.
Sea level at the last glacial maximum (roughly 20,000–30,000 years ago) was over 100 m (330 ft.) lower than today. For a taste of how significant a change that is, take a look at the Global Sea Level Rise Map which attempts to show the effects of global warming on sea levels. The maximum rise they have in their visualization is 60 m (just under 200 ft.) but you can see that even at 1/2 the extent of change relative to where coastlines were at the last ice age compared to baseline levels in recorded history, huge swathes of our most-populated areas would be under water.
Chances are, many, if not most of the older large human-occupied settlements of the paleolithic ended up under water. What we've had to study are the settlements of humans who moved into newly livable areas after the climate warmed up. Even without going into woo-woo "Atlantis existed!" territory, we can only wonder how many significant settlements were gradually covered by waves and lost to history forever.