There are two keys that are usually the problem ones to get. But as was already said, without knowing where you are it is hard to help you, but:
1) With the water level on the second level, go to the bottom level and go to where you met up with Ruto, go up to the second level in this room and blow up the crack in the wall to get a small key.
2) a little more complicated, you need to have gotten the Longshot after beating Dark Link. I can't remember which floor it is on, I think it is the first (someone correct me if I'm wrong, please!) there is a block you need to push, you can push it down a hallway a little bit, but then you hit a wall. You then have to go out to where you can see the eye underneath the ledge. Shoot the yes with an arrow, and then use the long shot to grab the target when the gate opens. This will then put you on the other side of the block. You can now push it the rest of the way out of the way, this will let you into another small room with a small key. I hope this is some help to you.