The standard fallback answer is that the "fountains of the deep" were opened, so there must be a lot of water underground. Now that we have a pretty clear idea of the structure of the earth, because of the way seismic waves travel through materials of different densities, that one no longer (

) holds water.
What the flood story does tell us is that the biblical authors had a very primitive understanding of the cosmos. They lived on a flat earth, and the sky was a dome, onto which celestial objects were attached. The entire thing was surrounded by a cosmic ocean. The Bible tells us that God simply opened literal floodgates and windows to let the water in.
This image has been misused by LDS prophets who treat the phrase "windows of heaven" as a metaphor for blessings. But no, it is a reference to literal windows.
I find it very entertaining when elaborate apologetics are used to explain simple myths. Meridian Magazine addressed the problem of how kangaroos and penguins made the two-way trip to and from the ark by claiming that angels carried them. OK, so why do you need an ark if angels can just levitate all of the animals?
I once had a discussion with Mrs. Hagoth about the problems of living for a year in a Jaredite barge with livestock, and all of the food and water that would be required. She offered that maybe God did something to accelerate time for them or that he put them into some kind of suspended animation for the duration of the voyage. My response was, "well, if He was just going to use magic anyway, why build boats at all? Why not just transport them across the ocean, the way Jesus got there in 3rd Nephi?"
“The easy confidence with which I know another man's religion is folly teaches me to suspect that my own is also.” -Mark Twain
Jesus: "The Kingdom of God is within you." The Buddha: "Be your own light."