While I believe that all water dungeons in The Legend of Zelda have their own merits, the one that always stood out for me in terms of puzzle design, atmosphere and sound design was the Great Bay Temple in Majora's Mask. But I guess I'll explain why I don't think the other dungeons I've played measure up.
The Water Temple of Ocarina of Time may be the most generic looking water dungeon to date, but it's understandable since Ocarina of Time was Nintendo's first stab at a 3D Zelda adventure. The developers were likely more focused on simply making a water-themed dungeon without worrying about making it multi-colored or trying to carve out more eye-pleasing shapes for the dungeon's architecture. It is infamous for being confusing, but I explained in an
editorial why players are exaggerating. The problem is that there is enjoyable gameplay to be experienced in the dungeon, but it's simply hidden behind a shroud of unconventional design choices: similar-looking hallways stretching in every direction on three different floors, a multitude of tiny rooms and a map that makes the player feel overwhelmed by the dungeon's perplexity.
The Lakebed Temple of Twilight Princess works with levers and aims for an ancient stone colossus of a dungeon that greatly resembles the style of the Zora's Domain. The flow of water must be altered to open up new paths, courtesy of the large rotating staircase in the center of the room. While I do believe that the Lakebed Temple has very creatively designed puzzles, the song that plays to accompany it isn't memorable nor catchy. It looks much prettier than the Water Temple and certainly doesn't lack atmosphere, but I believe that the Ancient Cistern and Great Bay Temple succeed Twilight Princess' water dungeon by far in that field.
Ancient Cistern is an intriguing concept. The Heaven and Hell levels might have seemed like an excellent during development, but the latter of the two worlds of Ancient Cistern was not emphasized nearly was much as the former and feels lackluster. The basement level could have been expanded and more detailed. Being a Japanese Hell, one would expect its enemies to be demonic... and they are, but only in appearance. The Cursed Bokoblins attack in hordes but are dreadfully afraid of the Whip and Sacred Shield. Slashing madly at the Bokoblins is enough to slay them, as they have no way to defend themselves. The upper level looks, sounds and feels like a sacred oriental palace brought to life. Its downfall is the under-utilization of its main item, the Whip and average dungeon design. After a second look, there isn't anything extraordinary about the way the cistern handles dunngeon progression. Climbing platforms and jumping across gaps is rewarding since the layout is creatively designed consisting of lotuses and rounded platforms.
Other water dungeons have unmistakable themes but the Great Bay Temple isn't simply an ominous, fish-shaped form surrounded by an eerie mist. The clangs of advanced machinery and pipes make for some interesting platforms, and the directions of flowing water has quite the effect on Zora Link as he tries to breeze through the underwater sections of Great Bay. Little does he know that power of rushing water makes entering the holes to other rooms a bit more difficult than he originally expected. What really sold the experience was the different colors of the pipelines, leading Link in the right direction. Not to mention that Gyorg is one of the truly indelible boss fights in Zelda, Great Bay Temple hovers near the top of my list of the most spectacular dungeons.