When you mean "chemical compound", then "eau" is uncountable, speaking generally; in French you say "indénombrable", (also) "non dénombrable", and also "non comptable" (Kalmbach).
It is more precisely a "nom indénombrable massique".
It becomes "comptable" by "découpe en unités" (nombre et noms massifs). For instance, mineral water as drawn from one spring is different from that in another spring; as such it becomes a unit and you can speak about "une eau minérale" and "les eaux minérales des Alpes" for instance; you have in fact the possibility to count the "eaux minérales" drawn from springs in the Alps.
When you speak about a body of water, as in "eaux territoriales", you still call "eaux" "indénombrable" or "non comptable" in French, but it should not be translated by "uncountable" in English. In English, "uncountable" is the French "massique" (Oxford Advanced Learner's Dictionary); see also "A Comprehensive Grammar of the English Language": "Non count nouns are singular and invariable". This type of noun ("indénombrable", in French) is more particularly called a plurale tantum (Wikipédia). The same term is used in English (pluralia tantum in s (thanks, looks, pains, etc.)).
This usage of "eaux" uniquely in the plural is found in connection with the drinking of the water of a particular spring because it is believed its water has some special qualities (healing, good for your health). This is largely a usage of the past but modern authors might still revert to it (boire les eaux).
(L'eau et le feu: la courte mais trépidante aventure de la ... - Bertrand Dardenne · 2005) couleur rouille : on boit alors l'eau dépurée . En prolongeant le temps d'exposition , l'eau devient inactive et perd ses qualités thermales . Le public et les curistes viennent boire les eaux , ferrugineuses et laxatives , " pour
There are cases where nothing can be said about the number of "eaux"; this is the case for the idiom "entre deux eaux"; this is so because you can't analyse this expression, it has a set meaning.
(Expressio : en manoeuvant entre deux partis sans se compromettre ; en refusant de s'engager ; sur une ligne de crète ; en évitant de se compromettre)