Les eaux has indeed the same meaning in French as Waters in English.

Depending on the context it can refer as you suggested to bodies of water.

Also, when a woman is about to give birth and her water(s) just broke French people say that “elle vient de perdre les eaux“.

"Water" as in English can designate a or some particular waters or water by its substance (same case as "fire", for instance).

Often, "l’eau" using singular is relative to the substance and often the plural is to indicate specific ones. But there is a plurality of meanings (please have a look here).

Some examples to illustrate the point, but please don’t forge a too strict opinion about them as we can surely imagine a variety of meanings using this word:

"L’eau est un élément composé d’hydrogène et d’oxygène" (substance)

"Les eaux nationales" (particular areas)

"L’eau s’est écoulée sur la table" (we are talking about a particular water, probably identified before)

"De l’eau s’est écoulée sur la table" (here the nature of water matters)

"L’eau du puit est consommable" (is particular but refers the nature of the water)

"L’eau de pluie est souvent polluée" (the substance)

"Les eaux de pluie sont souvent polluées" (the substance in its variety as they are inhomogeneous, also "rain" can be considered as particular areas too)

"L’eau terrestre est différente de celle de Mars" (the water in general)

"Les eaux terrestres sont différentes de celles de Mars" (the variety of waters that can be found on earth)

"L’eau thermale est bonne pour la santé" (thermal water is good for health in general, by its nature)

"Les eaux thermales sont bonnes pour la santé" (all thermal waters, whatever they contain, are good for health)

Also, “prendre les eaux” means go to a thermal city, like Bath in UK or Baden-Baden in Germany.