This one was a hard one for me.
It seems to be a reoccurring theme with the water temples to have a lot of puzzles. The entire dungeon is usually tedious, but not really difficult.
So here, I made my decision differently that I normally do. Instead of taking which water dungeon I enjoyed the most, or which one I loved to go through. I took the dungeon that i felt the best after getting through, and called that my favorite.
So for me, the Water Temple from OoT was my favorite. It took me so long to get through that temple, as I would sometimes forget to solve one of the puzzles, and so would have to drain the temple again, go through all those steps again, to try and find what I forgot to do.
But at the same time, this temple had my favorite mini-boss. Dark Link was, and still is, one of the best mini-bosses I've ever fought.
Beating that temple gave me a feeling of great self-accomplishment that I have not yet felt after any other temple.
The Water Temples are by no means my favorite temples out of all of them, though. But that's for a different thread, I suppose.