Water Temple is not the hardest temple.

[Paragon Fury]

The Water Temple was only considered hard for two reason:

In the old N64 version, there weren't a lot of clear markings to indicate where to go and what needed to be done, so it was easy to get lost.

It was also possible to accidentally use a key in the wrong place at the wrong time, thereby making the game unbeatable.

 

[Awexsome]

I haven't played the Master Quest version or anything but I remember the water temple being the hardest. I'm usually pretty good at figuring out stuff once I have the map and even moreso once I get the compass but god damn that water raising.

Each room has it's own 3 different versions based on the water level. Massive headache to remember how rooms change based on that. Plus, the Shadow Link mini-boss. Fuck the megaton hammer. Use the master sword only every time for epic duels.