The Water Temple wasn't hard at all, it was just annoying. A hard dungeon is completely different from an annoying dungeon. The puzzles and all of that weren't exactly the most challenging, but the entire dungeon itself could pester you a lot. Just because something takes you a long time doesn't mean that it's hard. In fact, the dungeon was probably one of the best in the series. I always liked the water theme for dungeons, and the Water Temple appealed to me a lot because of that.
Another thing I want to bring up... the Water Temple is actually easier if you play it on Master Quest. I know that Master Quest is supposed to make everything more difficult, but I honestly found no increase in difficulty from the regular quest to the other in the Water Temple, but instead found a decrease in difficulty.