-------THIS POST CONTAINS SPOILERS!!-------
Although the Water Temple is m most difficult temple, if I make a list f.om the least to the most difficult dungeon and temple, it would be like this:
8. Dodongo's Cavern (took me 1 week)
7. Spirit Temple (took me 2 days)
6. Shadow Temple (took me 3 days)
5. Jabu Jabu's Belly (took me 1 week)
4. Fire Temple (took me 1 week)
3. Forest Temple (took me 1 week)
2. Water Temple (took me, approximately, 16 days)
1. Inside the Deku Tree (I don't remember how long it took me)
Definitely, the Water Temple is my hardest temple: not because of the puzzles (in fact, most of the time I got confused because I didn't know a wall could be destroyed with a bomb and I couldn't find a key near a dragon statue, and because Shadow Link was to hard for me to beat), but because of the amount of backtracking, difficult portions filled with vortexes and annoying enemies, the constant changes between the Iron and Kokiri boots and the room right before fighting Morpha.
The Water Temple might have been difficult (16 days... although most of the time I had trouble with minor things), but the dungeon Inside the Deku Tree was insanely difficult at the time.
First off: it took me a lot of time trying to figure out how to go out of the room where you get the Slingshot... in fact, I figured it out some weeks later, so I saved the game and opened it again (that way, I had the slingshot and was out of that evil room)...
Second off: how was I supposed to know I had to throw myself to the spider's web to breaki it? I discovered that by accident, by accidentally throwing myself and magically seeing the solution to the puzzle...
I would include dungeons on the poll, as I would vote for that evil dungeon I mentioned above...