Genesis 1:6-8 - “ 6 And God said, “Let there be a vault between the waters to separate water from water.” 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 “sky.” And there was evening, and there was morning—the second day"

Introduction

Few people read this passage literally. It says that God created a vault marked by waters below and waters above. The vault itself is the sky. Logically then, the "waters above" are above the sky. But here is the part people miss: On Day 4, God places the sun, moon, and stars within the vault... below the upper waters.

We can see what appears to be a vault today, with oceans and land beneath, and a brilliant water-like blue above. Indeed, the sun even appears to be emdedded within it. Could seeing the sun in the midst of such brilliant blue have inspired a belief in the waters above?

Clearly, the sun is not actually within the vault, and there are no waters above it. So, if scripture is to be interpreted literally, what are we to believe?

One Flood-related Theory

One theory is that God put the upper waters from Day 2 above the vault... in Heaven basically. Later, He flooded the earth, letting all that water out in Genesis 7:11...

In the six hundredth year of Noah’s life, on the seventeenth day of the second month—

on that day all the springs of the great deep burst forth, and the floodgates of the heavens were opened.

Some back up this interpretation with Psalm 104:6...

You covered [the earth] with the watery depths as with a garment;
   the waters stood above the mountains.

Response

Psalm 104 describes the first 5 days of creation. The description starts in verse 2, and goes through each day in order. This places verse 6 within the description of Creation Day 1, not the flood. When you consider the literal wording of Genesis 1:1b and the science of Zircon Crystals, it turns out that verse 6 describes the earth on Day 1 quite well. There was a global ocean, and it covered everything.

As for Genesis 7:11, the flood gates may well refer to the upper waters of Genesis 1:6-7. However, those waters only had the appearance of being above the sky, but they never actually were; the upper waters were in the sky (or below it depending on your persepctive). Consider that in the creation account of Job 38, God made a cloud the deep's "garment, and thick darkness its swaddling band." It is the reason why God said "Let there be light", and it is why He separated the waters above (the clouds) from the waters below: the clouds were touching the ocean, like a garment.

Finally, the mere concept of an upper vault of water is an echo of the Egyptian creation myth that Moses would have grown up believing. The main differences between the Egyptian myth and Genesis 1 Day 4 is that Moses removed the Egyptian gods from the Genesis account, and recast the one true God as the creator.

Conclusion

Given the unlikelihood of the ancient Egyptians being inspired by God to believe in an upper chamber of water, it is much more likely that Moses was inspired to recast that myth in terms of God. Furthermore, it turns out that Moses' literal description, while not scientifically accurate, is a striking description of what the literal earth would have looked like to someone who did not know better. Conclusion: there was never any water above the sky.

If there were no waters above the sky, then Psalm 104:6 is not confirmation about how much water was above it. It is just another verse in the Psalm's description of creation. This particular verse fits in sequence with Day 1, and describes the initial conditions before God let there be light.

With no waters above the heavens, and Psalm 104:6 not describing the flood, the floodgates of the heavens in Genesis 7:11 are relegated to a description of how tulmultuous the flood's rains were, and not a description of where those waters were from.