The whole surface of the earth was once covered with water. Even the mountains were covered with water. We read that in Genesis 1:2: The earth was without form and void, and darkness was over the face of the deep.
This verse also makes one think about what happened during the flood, looking at Genesis 7:19: And the waters prevailed so mightily on the earth that all the high mountains under the whole heaven were covered.
This is an indication that the author of this Psalm was most probably thinking about creation as well as the later flood that came over the earth.
6 You covered it with the deep as with a garment; the waters stood above the mountains.