pfft, look at these scrubs. Water Temple? pah! FOREST TEMPLE? hahaha!!
I probably had the most trouble with
Great Bay Temple out of every 3D Zelda game, to be honest. Not sure what it was. Way more troublesome than OoT's water temple imo. I had trouble with 3 of the 4 Majora's Mask's dungeons, which is much more than I can say of any of the other 3D games.
Some others,
Skull Dungeon from
LttP. For some reason having all those different entrances to the temple really messed with my head.
Level 5 from
LoZ where almost every single room was filled to the brink with these guys
basically made me want to die.
then later on there's a dungeon that's filled with THESE guys as well
and perhaps worst of all isn't technically a dungeon/temple, but going through
Death Mountain from
Zelda 2 is by far the most painful and torturous Zelda accomplishment I've ever achieved. That is where the difficulty curve of the game goes straight up. If you played it you probably know exactly what I'm talking about.