No doubt about it: the Great Bay Temple was much harder. The Water Temple, while challenging in spots, had only one or two spots where I got stuck for more than a few moments. The Great Bay Temple, on the other hand, had me running all over the temple multiple times trying to figure out where to go next. It didn't help that I ran out of time and had to do several parts of it over again. Also, Gyorg is a lot harder than Morpha, and, while Dark Link was tough, you could always cheat and use the Megaton Hammer to beat him easily; the Great Bay Temple had multiple mini bosses, and at least one of them (the Gecko with the huge bubble thing) gave me almost as much trouble as the main boss.
Even though it was much harder, I think I liked the Great Bay Temple more. I guess I had about as much fun in the actual temple area there as I did in the Water Temple, but once I got the hang of fighting it, the boss was actually really fun. I really like fighting it as Zora Link: it adds a bit of challenge, and takes of bit of skill, which makes it all the more enjoyable.