The countable form used in the example, "waters" is poetic in use, and means "streams, rivers, lakes" collectively. Singular use in this sense is very rare, and archaic:
And as they went on their waye, they cam unto a certayne water (from an old translation of the Bible, in modern translations it is "river".)
In modern English this sense is only used poetically and only in the plural.
The plural can also be used for "regions of the sea" The territorial waters of the UK or "spa water" take the waters at Tunbridge Wells. In these senses it is always plural.
As a singular, it means "a serving of drinking water" *I'll have a water and a beer, please. But even in this sense, it is rather rare. "A glass of water" or similar would more common.
In nearly all other use, water is uncountable. Except in the rare cases described above, you don't use the plural "waters" or the countable singular "a water".
The word is unlike "fish" because "fish" is an acceptable plural of "fish". The only acceptable plural of "water" is "waters". The word "water" is singular, never plural.
The expression "a little water" is not a use of a countable noun "a water", it is the compound determiner "a little", which modifies the uncountable noun "water". Consider that you can't say "two little waters", because the compound word is "a little".