I think you're too rigid with your definitions. I just showed you an example of where water, usually not countable, is used in a plural form in real world usage.
Regardless of whether the noun is countable, the thing itself (water, air) absolutely is countable, i.e., comes in discrete measurable amounts, which is the more important issue here.
I am really confused why you think you can't count how much water is in your glass? Can you explain that?