The Water Temple was never nearly as hard as people like to make it out to be. It was really rather straightforward. It does take a slightly different kind of thinking to manage the water level, but it's not harder than saying "okay, I want to get to this part of the dungeon, so how do I get the water to a level from which I can access that part of the dungeon, and where is the path to the thing that gets the water level to where I need it to be?" It's really not that hard to find and remember where to go to change the water level and what water level that gives you and all the implications of each water level. It mostly just applies to the main room, anyways. Just make sure you cover each side path and you're good.
I'd say that the Great Bay Temple in Majora's Mask was way harder, because it requires you to use the water in a far more complex manner. You change the flow of water throughout nearly the entire dungeon rather than the level of water in the main room, which is much harder to translate into where you're able to go because it doesn't line up with the floors on the map, and the contraptions that change the flow of water are much more tricky to find and more confusing and complex to use.