Or to local flooding which would have ocurred everywhere at the end of the Ice Age. The glaciers etc would have sucked up a lot of water. When they melted, what had once been dry land would become seas or lakes. The humans living there would have had to migrate to higher ground and take with them a folk-memory of the rising waters which in due course became a story of a flood.

Either that, or it's an ancient memory of the Fall of Numenor! Take your pick!