Hidden throughout the land of Hyrule are six Great Fairy Fountains. The Great Fairies inside will give Link helpful power-ups and magic spells that increase both his offensive and defensive power.
In each Great Fairy Fountain, Link must stand on the golden Triforce emblem and play Zelda's Lullaby to awaken the Great Fairy and receive a new ability.
Death Mountain Peak
Reward: Spin Attack
The first Great Fairy Fountain that you are likely to encounter is at the top of Death Mountain. After obtaining Bombs and the Hylian Shield, journey to the mountain's peak. Find the flagpole nearby Goron City and climb the adjacent slope. Use your Bombs to destroy any boulders blocking your way. Soon after the mountain will begin to erupt, and shower you with debris. Equip the Hylian Shield and crouch to protect yourself, continuing only when the showers momentarily pause. You will eventually reach a wall which you are able to climb, but before doing so, kill any Skulltulas clinging to it. Once you have climbed the wall, you should find an entrance to Death Mountain Crater on the right, and a conspicuous rock wall on the left, with a sign post and owl in between. Use a bomb to destroy the rock wall and gain entrance to the Great Fairy Fountain.
Here you learn the spin attack for your sword and get a magic meter for it.
Hyrule Castle Grounds
Reward: Din's Fire
Enter the Hyrule Castle Grounds and climb the nearby vine to avoid the gate blocking your path. As you reach the gate, either go down the ladder into the guard room or jump off the gate roof. If you walk across you will be caught. From there walk up the road until the path branches. To your right should be a sign that says dead end and a boulder at the end of the path. Use your bombs to destroy the boulder and crawl through the passage to enter the Great Fairy Fountain.
This Great Fairy gives you the spell, Din's Fire, that will burn anything inside its attack radius. This spell is needed to complete the game. You need it to have access to the Shadow Temple.
Zora's Fountain
Reward: Farore's Wind
Go to the portion of Zora's Domain where Jabu-Jabu rests. As you enter, go on the right side of Jabu. Swim to a small peninsula behind Jabu with bushes and a lone tree on it. There will be a boulder next to the back wall. Place a Bomb next to this wall and the wall will be destroyed, revealing yet another Great Fairy Fountain.
The reward here is Farore's Wind, a spell that quickly lets you warp in dungeons.
Death Mountain Crater
Reward: Doubled Magic Meter
As an adult, enter Death Mountain Crater, preferably through Darunia's throne room. It is the fastest way and will allow you to reach the great fairy even if you don't have a red tunic. Once you enter take a right and walk across the bridge. Alongside the wall of the crater should be two boulders blocking a passage. Use the Megaton Hammer to destroy the boulders and the pathway to the Great Fairy's Fountain will be open.
This Great Fairy will double your magic meter, which will help in the future.
Desert Colossus
Reward: Nayru's Love
When you first reach the Desert Colossus from the Haunted Wasteland, look towards the right wall for two nearby palm trees. Be careful however, because you will be bombarded with an endless supply of enemies while you are on the sand. Between the two trees is a suspicious wall that can be destroyed with a Bomb. Lay a bomb down and the wall will be blown open, allowing access to the Great Fairy Fountain.
You'll get the spell Nayru's Love, which will allow you to cast a barrier around you. It takes twice the magic of the previous spells, however. Also you will still flinch from attacks.
Ganon's Castle
Reward: Doubled Defense
After completing the temple-related trials in Ganon's Castle and receiving the Golden Gauntlets, return outside the castle and find the dead end near many boulders. At the dead end should be a huge black slab. Use the Golden Gauntlets to lift this slab, revealing the final Great Fairy Fountain. This is good to use against Ganondorf.
The final Great Fairy shall increase your defensive power. Your hearts will have borders appear around them, and damage you take will be cut in half.