Weevil

Best answer as chosen by Asker / Ratings
There are 2 keys that most people usually miss. When the water is at mid-level, go back to the room where Princess Ruto was, surface, and bomb the wall.
The other key is inside the central building. Light the torch outside if you need to get back in. When the water level is at the 2F, sink to the bottom, go in the hole where the platform was, and kill the enemies.

There are 3 places where you can change the water level. The first place is where you met Princess Ruto, which will drain all the water. The second is inside the central building, which will raise the water to the 2F. You'll find the final one after taking the west door on the 2F and making your way back to the main room. This will raise the water level to it's highest.

Check out the question below for furthur details:-
Http://www.supercheats.com/gamecube/questions/thelegendofzeldaocarinaoftimemasterquest/105487/the-water-temple-as-and-adult.htm