Let's give God a little help and get Goron the Moron out of the story. You don't need a bunch of comets in this story, just knowledge of geological history.
The world started warming up around 17,000 years ago, with the ending of the cold part of our current Ice Age. The glaciers and sheet ice on Greenland and Antarctica, and much of the northern hemisphere, started melting off, as they'd done many times in the past. The melted ice caused sea levels to significantly rise. (Think of this like the current propaganda of global warming, only this time it was for real.)
The Atlantic Ocean's sea level rose, and flooded out the Mediterranean Sea. This apparently happened before mankind had developed written languages to record it. Then the Mediterranean Sea's sea level rose, and flooded into the Black Sea. This happened a few thousand years before mankind had developed ways of writing it down. But the event was significant enough that ancient stories of the flood were written down, and form the basis of ancient flood legends. It was written down too long after the event to be an accurate description of happenings, but it was too significant for the basic story not to be true.
