I had recently decided to replay Ocarina of Time (for the Gamecube), just finishing the Water Temple sometime ago. In all honesty, I find that one to be the most difficult, simple because I always miss a key that is very simple to get, but always easy to not remember. In all honesty, the temple itself is very simple and pretty straight-forward, it's just, the many many rooms and hidden areas you have to remember and find in order to get to certain places that irk me beyond belief. Dark Link can also be a nightmare, especially with no Big Goron Sword. Water Temple for Ocarina of Time is still the worst water themed temple in the series, in my opinion.
Great Bay Temple is fun for me, because, despite it looking difficult and complex, in reality it's also very straight-forward. Sometimes I forget to do a certain thing here and there, but it's pretty easy for me to beat it in under an hour or so. The mini-boss and Gyorg are very irritating, though, and I am guaranteed to always die at least once while fighting both (more so the mini-boss). Lakebed Temple... I have mixed feelings simple because it's confusing for me at times, and yet, it's not. I'm neutral for it, I suppose. The boss gets annoying, though.