Here's my whacko theory--maybe God beamed all of the water from sources in the solar system (Mars, Titan, etc.) in order to flood the earth and kill everyone, and then he beamed it back to whence it came.
Prove it didn't happen!
Kind of silly, hmm?
From Genesis 1:
[6] And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters.
[7] And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so.
[8] And God called the firmament Heaven. And the evening and the morning were the second day.
So basically; the sky is the firmament (even though Genesis calls it Heaven), the waters under the firmament are the lakes and oceans, and the waters above the firmament are what collapsed onto the earth from space causing the flood.
I saw once where somebody had done the math on what would happen if enough water to cover Mt Everest fell from space: it would have released enough energy to boil the oceans.
Anyways, this is what some people believe in regards to where the water came from. (I actually have friends who believe this, which is where I heard it in the first place).