There have been many, many approaches to making stop motion water effects work over the years, from baking powder, to hardened hot glue, to ripple glass, and everything in between. Stop motion special effects mad scientist Javan Ivey (who you know from his killer animation on Western Spaghetti, among other things) came up with one of the most unique ways to simulate animated water ever devised. The behind the scenes video is a zen experience, highly recommended with some Tchaikovsky or binaural beats (or both) playing in the background:

Here are a few classic examples of other water techniques explored in stop motion and sequences involving stop motion:

“Inspirace” by Karel Zeman, 1949:

“Frog and Toad are Friends” by John Clark Matthews, 1985:

“Elf” (animation by Chiodo Bros.) 2003: