This is the creation sequence with different meanings of water:
Gen 1:
1In the beginning God created the heavens and the earth.
2Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the
waters.
3And God said, “Let there be light,” and there was light.
4God saw that the light was good, and he separated the light from the darkness.
5God called the light “day,” and the darkness he called “night.” And there was evening, and there was morning—the first day.
6And God said, “Let there be a vault between the waters to separate
water from water.”
7So God made the vault and separated the water under the vault from the water above it. And it was so.
8God called the vault “
sky.” And there was evening, and there was morning—the second day.
9And God said, “Let the
water under the sky be gathered to one place, and let dry ground appear.” And it was so.
10God called the dry ground “land,” and the gathered waters he called “seas.” And God saw that it was good.
1. Water in verse 1 simply means the spirit of God/ the deep thoughts of God- He was hovering over darkness and emptiness. There was no earth or heaven or anything covered by H2O.
This kind of 'water' is also used here:
Pro 18:4
The words of a man’s mouth are deep waters; the fountain of wisdom is a bubbling brook.
Pro 20:5 The intentions of a man's heart are deep waters, but a man of understanding draws them out.
It shows God intended to create the universe and that the whole creation was drawn from His deep thoughts (wisdom & knowledge) and made manifest.
2. Water being separated from water - the water in the sixth verse also has nothing to do with H2O. It simply means space and the space above earth was what would be referred to as atmosphere and the one separated from earth is sky.
3. Only the third time (v9), do we get to see H2O.
Even here:
2 Pet 3:5 But they deliberately overlook the fact that long ago by
God’s word the heavens existed and the earth was formed out of
water and by water, 6
through which the world of that time perished in the flood. 7And by that same word, the present heavens and earth are reserved for fire, kept for the day of judgment and destruction of ungodly men
Peter implies that the word of God is deep waters.