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This may be the passage you are thinking of roamer:

Psalm 33:7
He gathers the waters of the sea together as a heap;
He lays up the deep in storehouses.

Here are some other relevant passages:

Genesis 1:6-8
Then God said, “Let there be a firmament in the midst of the waters, and let it divide the waters from the waters.” Thus God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament; and it was so. And God called the firmament Heaven. So the evening and the morning were the second day.

The firmament mentioned above is the first heaven, which is the sky. Second heaven is outer space. Third heaven is the heaven of heavens which is where God’s throne is. Clearly, at creation God placed water above the atmosphere.

Genesis 2:5
before any plant of the field was in the earth and before any herb of the field had grown. For the Lord God had not caused it to rain on the earth, and there was no man to till the ground;

Genesis 7:11
In the six hundredth year of Noah’s life, in the second month, the seventeenth day of the month, on that day all the fountains of the great deep were broken up, and the windows of heaven were opened.

Genesis 8:22
While the earth remains,
Seedtime and harvest,
Cold and heat,
Winter and summer,
And day and night
Shall not cease.

The passage above shows the seasons began at the flood. Other things changed such as granting people to eat meat for food, instituting the death penalty for murder, and the shortening of the natural human life span.

2 Peter 3:5-6
For this they willfully forget: that by the word of God the heavens were of old, and the earth standing out of water and in the water, by which the world that then existed perished, being flooded with water.

The expression “out of the water and in the water” above refers to the earth having oceans and seas (and also before the flood something called the “great deep”) and a mass of water above the earth (i.e. above the atmosphere.