Albert Barnes Commentary Psalms 104:6

"Thou coveredst it with the deep as with a vesture; The waters stood above the mountains." — Psalms 104:6 (ASV)

Thou coveredst it with the deep as with a garment. Compare the notes at Job 38:9. The meaning is that God covered the earth with the sea—the waters—the abyss—as if a garment had been spread over it. The reference is to Genesis 1:2. In that account of the work of creation, what is there called “the deep”—the abyss (the same Hebrew word as here, תהום t e hôm)—covered the earth. It was what “appeared,” or was manifest, before the waters were collected into seas and the dry land was seen.

The waters stood above the mountains. Above what are now the mountains. As yet, no dry land appeared. It seemed to be one wide waste of waters. This does not refer to the Deluge, but to the appearance of the earth at the time of creation, before the gathering of the waters into seas and oceans (Genesis 1:9). At that stage in the work, all that appeared was a wide waste of waters.