- Anime battle in water.
-Battle vs Clair in Johto.
In the Anime, the Trainer basically stands on a base outside of the water and the Pokemon (having to be able to stay in water) will be inside the water. This is what happens in the anime. You can watch this in these episodes:
(These Numbers aren't exact for the whole series, just for every generation.)
Ingame, you are not shown while the Pokemon play the moves, but I think it would be similar to the anime, just...that your Pokemon will be shown standing on a blue circle which represents the water.