The fountains also of the deep and the windows of heaven were stopped, and the rain from heaven was restrained;The flood was not only caused by rain for 40 days and 40 nights, it was also caused by the opening of the windows of heaven and the fountains of the deep. I believe the windows of heaven consist of the earth's atmosphere, protecting the earth from meteorites, the sun, so on and so forth. It's possible that a meteorite could have busted the earth's foundation, springing forth the fountains of the deep.
Just as it could have happen then so could it happen in the end as described by Isaiah:
And it shall come to pass, that he who fleeth from the noise of the fear shall fall into the pit; and he that cometh up out of the midst of the pit shall be taken in the snare: for the windows from on high are open, and the foundations of the earth do shake. The earth is utterly broken down, the earth is clean dissolved, the earth is moved exceedingly. The earth shall reel to and fro like a drunkard, and shall be removed like a cottage; and the transgression thereof shall be heavy upon it; and it shall fall, and not rise again. Isaiah 24:18-20