As someone posts beneath the article there have been radical shifts in the sea levels and in the shape of the land over time.
The melting of the ice at the end of the ice age may have caused the deluge, which is mentioned in many different cultures, to swamp large tracts of land.
Other civilisation got hammered by various things eg Minoan (possible tsunami), Mycaenean (possibly invaded by the 'sea peoples')
Anythings possible
Here's an interesting device that was found under the med:
The antikythera mechanism which was far more advanced technology than people had previously thought was possible for that time:
http://en.wikipedia.org/wiki/Antikythera_mechanism