Water Temple is definitely the hardest, I don't care what anyone says. Even if you didn't find it as hard as some of us did, it is still more difficult than any other dungeon. I mean....
Deku Tree: Please
Dodongo's Cavern: Creepy at first but not actually hard
Jabu-Jabu's Belly: The electric element makes it more difficult and the layout is complex, but at the end of the day it's still not that bad
Forest Temple: I would say second-hardest dungeon, though I find it harder in a stealth sense than in an actual action sense
Fire Temple: This has always been a walk in the park for me, I'm amazed Pancake that you find it hard :O
Shadow Temple: Scary, yes, hard? Well, the first time yes, but I find when you've done it once it's ok.
Spirit Temple: Fun, but simple
Ganon's Castle: Pretty easy, to be honest, especially for a final dungeon.
The Water Temple however? Hard puzzles, hard action (maybe not Morpha but Dark Link certainly is if you've got lots of heart containers anyway), even the minor enemies have a habit of jumping out at you. You have to swim, which is a pain in the *** in any dungeon. The iron boots make you slow. You have to change the water level what feels like a million times even if it actually isn't that many times. It takes the longest, and at least in the original version, every single door looks the same. Some of the keys are also hard to find. Challenges around every corner, you never feel quite safe, unlike in the other dungeons.
I would have to say that the water temple is the hardest for me. It's not that it's more difficult as such, more that it is so infuriatingly tedious that I find it difficult to actually continue playing past that point. I never want to actually go inside. I waste hours upon hours finding heart pieces and going over every little side quest
Oh my god I do the exact same thing, and I think I find it hardest for the exact same reason