And darkness [was] upon the face of the deep. And the Spirit of God moved upon the face of the waters.

from Holy Bible (KJV) – Genesis 1 on Rap Genius

Notice the “face of the deep” / “face of the waters” parallelism, which is a literal translation of the Hebrew “pnei” (פני)

The “face” of the waters/the deep simply refers to the surface of the waters.

To help improve the meaning of these lyrics, visit "Genesis 1" by Holy Bible (KJV) and leave a comment on the lyrics box