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See my answer to the question about the firmament. Calling it a "vault" is a bad translation of the Hebrew word, which connotes something thin and stretched out to cover a wide area. God placed an expanse between the waters that were on the Earth (rivers, oceans, lakes, etc) and the waters that were above the earth (clouds).
When the Flood came, all we know is that all the water that was necessary to do the job was employed to flood the Earth. we aren't told where it came from. I've heard speculation that, as this was a miraculous and unique event, God could have brought in extra water that doesn't ordinarily belong to Earth and then sent it away again. But that's just speculation, and we don't really have any way of knowing for sure.
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Massive 'ocean' discovered towards Earth's core Posted by Bernard Alvarez on June 21, 2014 at 11:06am
[separating the water from the water]. So what is a near Hebrew word for 'sky' that may have been erroneously mistranslated?
6 And God said, βLet there be a vault between the waters to separate water from water.β 7 So God made the vault and separated the water under the vault from the water above it. And it was so. 8 God called the vault
Read more: http://thegic.org/profiles/blogs/massive-ocean-discovered-towards-earth-s-core#ixzz35TJGsLpl
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There is a very good explanation of where most of the water came for the flood in this link Explanation of Noah's flood This explanation would give plenty of water to flood the earth.
I do not believe the universe is made of water,but there is evidence of vast amounts of water out there in this link.water on the edge of universe
There are lots of very good material to give a good explanation of the world.And I do not believe God is the author of confusion. Satan is!