I think I need to play the N64 version of this game some time. The Water Temple in OoT: 3D wasn't actually that bad. Just a bit annoying^^
It wasn't that bad, just generally confusing from what I remember. This was about 13 years ago, though. And I let my friend borrow the game and apparently there is way to actually get stuck in the water temple and he managed to do it. Nothing he could do but start completely over.