Morpha

Giant Aquatic Amoeba: Morpha (水棲核細胞モーファ, Aquatic Cell Nucleus: Mōfa) is the Boss of the Water Temple in Ocarina of Time. Probably created by Ganondorf once he acquired the power of the Triforce, it has complete control over the water in the room in which it resides, moving swiftly through it and creating long water "limbs". This monster is responsible for the state of Lake Hylia as well as the frozen condition of Zora's Domain.

Strategy
This creature may seem to be a fearsome tentacle made of water, but in all actually it is only a bouncing red ball. This ball is Morpha itself. The advantage it has is that it can manipulate the water in any way it likes, creating one (and eventually two) large water tentacles. These tentacles try to grab Link, squeeze him, and toss him toward the spikes surrounding the arena. It is the best idea to try to avoid the tentacles when they lunge forward and focus on the core. When a tentacle lunges forward, use the Longshot to grapple the core and pull it towards you. Once it is right in front of you, use the Master Sword and slash it. (If you can, try to keep the core on dry land and keep slashing it. Or better yet, trap it in a corner and completely ruin its day.)

Keep repeating this process. It will eventually summon a second tentacle, but this is not that much of a big deal as long as you avoid it. Just keep focusing on the tentacle with the core in it. When Morpha is defeated, the core will burst in a spray of water. The tentacle will cling to life as long as it can, using up all the water in the central pool. Once it uses up all the water, it will drop to the floor and splatter.

Link's rewards for this victory is a Heart Container and the Water Medallion.

Trivia

 * Bear in mind that this battle CAN be completed with the Hookshot as opposed to the Longshot.
 * Din's Fire is capable of evaporating Morpha's tentacles, a useful trick in a bind.
 * Morpheel is a reference to Morpha both in the way its first stage is defeated and in name.