Lakebed was a cakewalk; it had the water temple feel to it but in execution it felt like any ol' dungeon. Loved the BGM however. Great Bay is really, REALLY simple if you get the pathways down. The miniboss (the giant eye thing?) takes arrows and a sword + spacing – had MM been a fighting game I could buffer all attacks and finish him taking no damage. Gyorg is a mess though, you really need to have a good grip of swimming around and know escape routes, or else he'll eat you up and you could face several game overs... Water Temple (OoT) is even simpler than all three of these if you know the rule of "bottom up". Sure enough, keys are hard to get...if you don't know where you're going. There are very little obstacles in the WT, but it features the most awesome boss of Zelda history IMO – Dark Link. Morpha was a joke.
The hardest? Great Bay Temple for sure. The most frusturating? I almost want to say Lakebed Temple.
The Water Temple is really easy in my opinion, so that's just out. The others I haven't played many times, but there's no way Lakebed is hard.
But Great Bay Temple I found to be a nightmare with the water flows. Now, once I manage to learn the mechanics of it, it might be so bad, but only having gone through it twice makes that a little difficult. Plus it has the hardest boss out of the three.
Ancient cistern from SS is one but you have not played it so you would not know. Great bay is the hardest. Changing the water flow is complicated and the puzzles hard and the boss fun and insanely difficult.
I have some memories of asking my older brother to finish the Water Temple in Ocarina of Time when I was 5. I used to find it too hard since you have to think three-dimensionally to get the hang of it (like when you have to get the key under the platform).
I think that's one of the main problems people had with it when the game was originally released and I wouldn't be surprised if it was, since it took dungeon design for the series a step further by showing off what Nintendo could pull off with 3-D structures and a little bit of imagination (and maybe some degree of sadism because a lot of people hate it lol). I've called it a favorite among dungeons because of how it built on the additions A Link to the Past made to the series (namely, multi-leveled dungeon design) to make an infamously complex design. I can see why some people wouldn't find it hard, though, since the later games kept building on that. There's also the changes they made in Ocarina of Time 3D.
Now, I didn't think either Lakebed Temple or Great Bay Temple were as hard, but maybe that has to do with the fact that I had a fair bit of experience by the time I played through those. Maybe I did get stuck in Lakebed for a while, but not for too long as far back as I can remember.
The next is about Great Bay Temple. I mention the boss, which is why I put it in a spoiler tag:
Gyorg is the highlight in Great Bay's difficulty, in my opinion. But I guess you just have to master the Dolphin Jump to get some advantage (and maybe the extended magic bar or a Chateau Romani, just in case).
In case you want to see a near-perfect dolphin jump, skip to 1:46 in this video.
I had recently decided to replay Ocarina of Time (for the Gamecube), just finishing the Water Temple sometime ago. In all honesty, I find that one to be the most difficult, simple because I always miss a key that is very simple to get, but always easy to not remember. In all honesty, the temple itself is very simple and pretty straight-forward, it's just, the many many rooms and hidden areas you have to remember and find in order to get to certain places that irk me beyond belief. Dark Link can also be a nightmare, especially with no Big Goron Sword. Water Temple for Ocarina of Time is still the worst water themed temple in the series, in my opinion.
Great Bay Temple is fun for me, because, despite it looking difficult and complex, in reality it's also very straight-forward. Sometimes I forget to do a certain thing here and there, but it's pretty easy for me to beat it in under an hour or so. The mini-boss and Gyorg are very irritating, though, and I am guaranteed to always die at least once while fighting both (more so the mini-boss). Lakebed Temple... I have mixed feelings simple because it's confusing for me at times, and yet, it's not. I'm neutral for it, I suppose. The boss gets annoying, though.