In the thread "Evidence for a recent flood", claims have been made as to the sources of the water of the flood, the "fountains of the deep" amongst other sources.
The deep: tĕhowm. It is the same word as in Genesis 1:
quote:And the earth was without form, and void; and darkness [was] upon the face of the deep. And the Spirit of God moved upon the face of the waters.
So what is the deep? Other near Eastern religions had the world starting as just water, the Genesis account seems consistent with this. The face of the waters just exists at the start of Genesis, it is never explicitly created. Theological arguments may be made for god creating the deep, the waters, but that's for another time.
Either way, god created the firmament and put some of the waters of the deep on one side of it, and put the rest underneath the firmament. He then moved the water around to reveal dry land, thus explaining where the water we presently have came from.
The flood waters came from holes in the firmament which held back some of the waters from the deep. And from the 'fountains of the deep'. A world we are separated from by the firmament. How they thought these fountains worked is anybodies guess. Where they fountains tapping into some of the deep that is below the land? Where they fountains in the firmament? I don't know.
So that's where the water came from: the primordial state of everwater called the deep.
Where did that water go? There are two possible answers. The first is the simple reading: The water dried up. The people that wrote this story probably did not realize that when water dries up, it goes somewhere.
A second answer, which does not assume its a plot hole resulting from scientific ignorance, would be that the water presumably returned to the deep. It evaporated back up through the firmament. Presumably the stoppers Yahweh used were semi permeable membranes or something. Or maybe it drained into the large cavernous underworld?
Personally: I think they just thought it dried up and was thus accounted for.