Of all games I played with a Water Dungeon:
4. Water Temple- It's difficulty is easily overrated. I feel it's a lot more linear than people make it out to be.
3. Ancient Cistern-I was a bit confused at first, but then I came through and the rest of the dungeon was pretty linear, like most dungeons in Skyward Sword.
2. Lakebed Temple-The water systems and the main room of the dungeon are much more discombobulating than the easy Water Temple's. For a good 3/4 of the dungeon, navigation can be a challenge.
1. Great Bay Temple-The truly hard water dungeon. The water system here is the most complex, changing the direction of the current and making sure that all the pipes are running proved to be an arduous task. I sometimes found myself backtracking to return to pipes I hadn't activated.