Water Temple (Ocarina of Time)

Deep under the vast Lake Hylia lies an ancient temple known as the Water Temple. Link must use the Iron Boots and the Hookshot to access its entrance by shooting the target above the gate. Various parts of the temple require Link to go underwater for substantial amounts of time, thus necessitating the Zora Tunic (though the Water Temple can be beaten without it by an experienced and resourceful player). Its enigmatic structure consists of various levels and requires the use of playing Zelda's Lullaby at each of the special markings on the walls. Link will need to use all of his intellectual skills and cunning survival techniques to truly conquer this temple. Link will also come to confront his very own shadow-self in the Water Temple. After defeating Dark Link, Link will find the Longshot. Once he acquires it, he can get the Boss Key and enter the lair of the aquatic boss, Morpha.

This is often seen as the hardest temple that Link will come across in the game and possibly one of the hardest in the entire Zelda series.

Master Quest
Ironically, the Water Temple makes much use of Din's Fire in the Master Quest version of the game. The Hookshot is also used more than in the original version. The map, compass and even the Longshot are obtained really early in the dungeon, the latter giving access to a lot of new areas and making most puzzles easier than before. Most rooms are blocked with gates, so a puzzle must be solved to be able to access them. Boulders and most enemies are no longer found, except for two Spikes and eight completely new Stalfos. Two curious new features are a room with several Dodongos and several crates that are found throughout the dungeon. Only two of these crates are somehow important (one contains a Small Key and the other hides a switch).

Minor Enemies and Traps
Blue Tektites Shell Blades Keese Stingers Spikes Like Likes Sink holes Whirlpools Blade Traps

Trivia

 * Due to the frustrating swimming mechanics and the incredible length, many regard the water temple as the most annoying dungeon in Ocarina of Time, and some the most difficult Zelda dungeon yet. Compounding this perceived difficulty is the need to pause the game in order to equip or unequip the Iron Boots, adding a lot of extra time to the dungeon. Ironically, the Water temple is actually easier on Master Quest. The infamous "serpent-shaped" room now has Hookshot targets over the wall, making it easy to simply bunny-hop through the vortex-filled gauntlet.
 * It is very likely that the Water Temple and the Lakebed Temple of Twilight Princess are the one and same.
 * If the player goes first to the Shadow Temple and gets the Hover Boots, they can beat this dungeon much more quickly (less than 10 minutes), as shown here. It should be noted, however, that it is impossible to enter the Shadow Temple before beating the Water Temple without glitching.
 * A surprisingly-little-used strategy helping greatly in the Water Temple is using Farore's Wind at doors near the water rising tablets, then warping back when they are required.