There are countless definitions of any word. "Waters" has plenty of definitions, and even a verb form ("he waters the plant"). In my original post, I was not contesting any definition of any word, but pointing out the grammatical contradiction /u/Lore_Wizard made after insisting that the noun should be treated as a mass noun rather than a count noun. If you are going to insist that the uncountable form of a noun is used, it is contradictory to then say that it can also be plural.

Regarding the usage of the word in your specific example, I interpreted "waters" to be a singular term for "all of the water" (because the passage is describing things in terms of the grand scale at which God operates, I interpreted "waters" to be equivalent to saying "the totality of earth's water", which, although a stretch, would in fact be the singular sense. Admittedly, this singular form is probably very uncommon, but I'd argue that it's a matter of personal interpretation.) In my first reply to you, I implied that your example is necessarily singular, and that the plural count noun sense could be used only if you wish to refer to one "water" as "a single molecule of H2O". Operating under the broader assumption that one "water" is equivalent to the abstract concept of "a non-specific sized area of water", it was wrong of me to imply that the example cannot plural. Everything else I said holds up, I believe.

I'm sorry if this didn't clarify things or if I have misrepresented some grammatical concepts. I don't know a whole lot about formal grammar, but I have quite a strong intuition about it, so when something is off, it jumps out at me. But then I'm not always sure about how to go about explaining myself :P