Depends on if you're using water to include types of water (if, like a maniacal madman, you have mixed Evian, Buxton and Harrogate mineral water into one jug). Then 'i mixed fewer waters' or 'there are fewer waters in that glass' would be valid.
To be clear: I'm not the person you replied to, just someone who finds it quite interesting (in the same way that the plural fishes is valid if you're talking about different species of fish).
And yes, I know prescriptivism is bad, but also it is quite fun.
Eh, you wouldn't use the noun water to refer to atoms of water. 'How many waters are there?' to refer to atoms of water is the statement of someone deranged