To the writers and readers of this text "the waters" would have meant, first and foremost, the primal element. Not the literal stuff floating in puddles.
The correct analogy for a person from 2020 would be "chemical elements", or even "atoms and molecules".
Interesting perspective. It's certainly worth keeping in mind that words from ancient texts may have had meanings that we currently don't recognise anymore. This sounds quite plausible.
The correct analogy for a person from 2020 would be "chemical elements", or even "atoms and molecules".