First of all, I'd never use water in the whole level, but only in a small bottom part of it. And even then, the facts mentioned might add strategy, but definitely remove game flow and fun. If it's not necessary to travel through the water, people will avoid it because of the mentioned problems when moving in water, and if you would be forced to move through water by getting from each base to the other, or to the carror or w/e, then people might get annoyed by it. Thus, as a conclusion, you might use water, but not as much more than a decoration (or like a 1-tile-high water area using that 1-tile water event thingie, like e.g. in tilesets like jungle and agama's jungle tileset of which i forgot the name now) if you don't want to heavily influence the gameplay of the level.