I'll have to go off my experiences here...
To be honest I'm on eof many that struggled on the infamous Water Temple first time round, mainly due to me missing two keys and that's the thing with this dungeon, missing one key can really screw you over. The Great Bay Temple on the other hand I handled quite efficiently, I completed the dungeon relatively quickly and without too many moments were I became lost.
Judging the two from a neutral perspective though; both are similar difficulty wise, the element if water makes traversing that bit more complicated, you have the general restriction of water, it's not as simple as walking etc. However the biggest factor that the two dungeons revolve around are the manipulation of water. The two actually handle this in two different ways, the Water Temple included lowering and raising the water while in the Great Bay Temple you simply change the current. Now for me the Water Temple was definitely the more tedious however this was due to the design of the dungeon itself. The layout alone made this dungeon extremely complicated for a typical dungeon, multiple rooms on three alternating levels which revolve around a central structure. The sheer complexity of the layout made the manipulation of water much more difficult, one couldn’t just simply lower and raise the water, you had to go through quite a lot of lengths in order to do so and you would have to plan strategically which level you would go to in order to reach your destination. The Great Bay Temple had a rather simple layout, the task to change the currents was more challenging however changing the currents and navigating fro this was much easier, just follow the correct path and enter the rooms available. Since there was only two possibilities it made things much less complex.
Both had their fair share if individual puzzles however I feel the Water Temple slightly edged it on the difficulty scale, this was probably due to the idea of finding keys how within fits into more of the exploration aspect of the dungeon. The Great Bay Temple however had the better puzzles for me, all in all though the Water Temple and the more complex of the two, in my experience anyway.
However there could be a twist, if you consider the stray fairies then this raises the dungeons difficulty quite a lot. I found this dungeon to be the harder out of the other three in Majora's Mask in terms of finding and collecting all 15. Some were hidden in quite obscure locations and one could easily miss them making find them all a harder task all together, some also raided the puzzle and the longevity of the dungeon all together. However I would still say the Water Temple wins here, take out the inefficiency of switching to iron boots and you have a dungeon that is very complex with tough navigation and one that boasts some pretty challenging puzzles.
nion:.
