The water boss basically is a timed battle, so the mechanics are a little different. When you go in the boss room, there's a gauge on the side showing the water level, and it'll slowly go down over time. Every now and then, the boss will pop up on either the right or the left side of the screen (you can figure out which by watching where it swims) and start horking up goop, causing the gauge to start going back up again. Just whack or shoot the boss to make it stop.
Oh, also, try not to fall in the water; it won't actually hurt you all that much, buuut it will delay you when you're trying to get to one side or the other in a hurry. This is pretty much the one single part of the game where platforming skills actually matter vOv
Note that you don't need to go nuts trying to hurt the boss however you can, you can't actually kill it with damage, just interrupt it when it's coughing crap up. Don't even bother trying to hit it when it's zooming around.
-Do- hit the pillar thingies that stick up out of the water.
