Water is always tricky in animation. Here's some suggestions:

A pond or pool of still water: use a mirror embedded into the "ground" set

Ocean water : crinkled cellophane

Waterfall: clingwrap, cellophane and shaving cream

White water rapids: shaving cream

Mysterious swamp: dry ice ( works best if it's a live action shot though as the dry ice vapor will dissipate  quickly)

Underwater shots: sometimes you can just paint the backdrop the color of the water and have your character in front of it. Bubbles will help sell it that it's underwater, and bubble scan be added in a number of ways, or the shot could be taken as a live action puppetry effect, in a glass water tank, and pump real bubbles through the water.

( That's a bit of a "cheat" because then it's not really animation. But if it's about telling a story, you would pick the best technique to do the job, whether that means mixing some live action effects, or some Computer Generated effects, into the mix.)