Genesis 1:1-2 accounts what was before God gave form to the Earth, and that is water:
1 In the beginning God created the heavens and the earth. 2 Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.
— Genesis 1:1-2
Now that might be interpreted as a metaphor for "vastness", maybe, but other verses in Genesis also seem to assert the same thing:
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.
— Genesis 1:6-8
In those verses it is described how God separates water. The separation is called "sky" (this will be relevant later, that's why I made it bold). It also says there is water both under the sky (on Earth) and also above the sky (in space?).
Furthermore, in the account of Noah's Flood, it is described how God opened up the "sky" (among other means of flooding the planet).
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. 12 And rain fell on the earth forty days and forty nights.
— Genesis 7:11-12
The question:
Obviously it makes no sense to say the universe is full of water. What does the word mean then, in those passages? What is it used as a metaphor for?