I wouldn't exactly say it's hard, it's actually just annoying. You have to constantly raise/lower the water level, nearly each key requires a change in the water level, also. Not to mention some rooms you have to visit more than once at different points in it just to get the keys you need.
A problem I had with it was always forgetting a key and taking awhile to figure out which of the chests on the map it was, what water level I needed for it, and then actually getting to it. But, like I said, it wasn't hard; Just annoying.
Morpha was about the same story. Mainly with trying to hookshot that blasted eye, not to mention if you couldn't do it, you still had to get out of the way so you don't get grabbed and thrown.
So as a whole, it was just a giant pain to deal with and it probably always will be to me until the one time I get through it without having to backtrack more than required.