The OoT Water Temple is very like the 3 last dungeons in Majora's Mask. There is a somewhat linear path, a logic pattern to follow in the whole dungeon. If you aren't focused enought, and loose this path, you will be lost and here is where the problems starts. In short, you better do it entierely in 1 time.
For my part, I'm revising my advice on the women in Twilight Princess who give you vision of the hearts piece containers. Since yesterday I was thinking it spoil you from searching the heart containers.
Now I have 1 piece of heart missing in OoT3D and I want it before starting Master Quest, but even if I know the game by heart I don't know what piece of heart I didn't get. So there is 36 things to check with a list online. Not funny.
We were discussing sometimes on GAF on how the rupees system is useless (not too many things to buy generally in Zelda games), but maybe, later in the Zelda games, you can give many rupees (like 200 or 300 rupees) to a women in order to get a vision about the remaining pieces of heart. Later in the game don't spoil you, many rupees makes a good use of your money, and it helps you to get 100% more quickly in the end of the game.