(This is what came into my head so hope it helps...maybe i don't exactly know where you are or what part of the Dungeon)
Ah.. Jabu-Jabu's belly. He is a trick, lower the water level, go back into the room where you need to hookshot the diamond shaped rock into the buttons then get the key, if that does not help then try this, right besides the boss room, to the right to be precise,(somewhere in the right side of where the boss room is) the is a big Black hole to the right of it there is a hiden chest try to get it. if all else fails check the map retrace your sterps, search the room CAREFULLY. you might have MISSED a room, people get lost in Jabu-Jabu's belly a lot since they don't check the place very well