The most helpful tip I can give you is dungeon map dungeon map dungeon map! Make sure you get the dungeon map at all times! Try looking at any room that you haven't gone into before, look around, try switches, and don't be afraid to lower/raise the water level!

The water dungeons in all of the Zelda games are confusing, and you REALLY want to try being as methodical as possible, and not unlock doors left right and center. Look everywhere in the areas you have access to. Is there anything there that you haven't solved yet, any undone puzzle? Any point you haven't realized you can hookshot up to?

And don't be afraid to cast Farore's Wind at your current point in the dungeon, and leaving to do some sidequests to cool down. The warp points stay as long as you don't cast another Farore's Wind.