Shooting something in the water isn't just an ethics issue, it's also a saftey issue. Bullets can ricochet off of water very well and travel very far. Hunters safety 101, never shoot a bullet at a body of water.
Having said that there is some common sense that comes into play. If an animal is standing say knee deep in a small cattle watering hole and there is a good back drop I'd take the shot. If the animal is swimming in pond or a lake, no way!