a. flowing water, or water moving in waves: The river's mighty waters.
b. the sea or seas bordering a particular country or continent or located in a particular part of the world: We left San Diego and sailed south for Mexican waters.
Waters | Define Waters at Dictionary.com
The word "waters" is also used in a number of idioms. Examples:
"muddy the waters" -- to make something like an issue or situation more confusing
"still waters run deep" -- you say this about a person who's very quiet but has an interesting personality or interesting thoughts
"(to) test the water(s)" -- find out if something will be successful or if would you like it before you try it