The “fountains of the great deep” are mentioned before the “windows of heaven,” indicating either relative importance or the order of events.
What are the “fountains of the great deep?” This phrase is used only in Genesis 7:11. “Fountains of the deep” is used in Genesis 8:2, where it clearly refers to the same thing, and Proverbs 8:28, where the precise meaning is not clear. “The great deep” is used three other times: Isaiah 51:10, where it clearly refers to the ocean; Amos 7:4, where God’s fire of judgement is said to dry up the great deep, probably the oceans; and Psalm 36:6 where it is used metaphorically of the depth of God’s justice/judgement. “The deep” is used more often, and usually refers to the oceans (e.g., Genesis 1:2; Job 38:30, 41:32; Psalm 42:7, 104:6; Isaiah 51:10, 63:13; Ezekiel 26:19; Jonah 2:3), but sometimes to subterranean sources of water (Ezekiel 31:4, 15). The Hebrew word (mayan) translated “fountains” means “fountain, spring, well.”1
Fountains of the deep scene taken from "The World That Perished"
So, the “fountains of the great deep” are probably oceanic or possibly subterranean sources of water. In the context of the flood account, it could mean both.
If the fountains of the great deep were the major source of the waters, then they must have been a huge source of water. Some have suggested that when God made the dry land appear from under the waters on the third day of creation, some of the water that covered the earth became trapped underneath and within the dry land.2