There are several things that confirm that the "deep" in Gen 1:2 are deep waters and not just a deep hole.
1. Parallelism of the Gen 1:2
Now the earth was formless and void,
- and darkness was over the surface of the deep.
- And the Spirit of God was hovering over the surface of the waters.
Note the repeated parallel use of "over" (עַל), and "face/surface" (פְּנֵ֥י)
2. Day #2 Separation
We observe that on day #2 of creation week, God separated the waters above from the waters below. [Note that God did not create the waters on day #2 as they had been created at a previous time, but simply separated them.]
Further, on day #3, God separated the dry ground from sea to create arable land.
3. The word "deep", תְּהוֹם , is always associated with deep water in Genesis
Here are the other three times the word תְּהוֹם (= "deep") occurs in Genesis
- Gen 7:11 - In the six hundredth year of Noah’s life, on the seventeenth day of the second month, all the fountains of the great deep burst forth, and the floodgates of the heavens were opened.
- Gen 8:2 - The springs of the deep and the floodgates of the heavens were closed, and the rain from the sky was restrained.
- Gen 49:25 - by the God of your father who helps you, and by the Almighty who blesses you, with blessings of the heavens above, with blessings of the depths below, with blessings of the breasts and womb.
Further, we see the same association in later writings as well such as: Ex 15:5, 8, Deut 8:7, 33:13 (This is all the places in the Torah), Job 28:14, 38:16, 30, 41, 32, Ps 33:7, etc.
4. Peter tells us that God began creation week with Water
2 Peter 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
Thus, there can be little doubt that "deep" in Gen 1:2 refers to deep water. Indeed, of the 36 occurrences of the word "deep", תְּהוֹם, it never refers to a deep nothingness - most often deep water but occasionally a deep earth below mountains.