Great Fairy Fountains-The Great Fairies throughout Hyrule give you different spells, and abilities that Link uses throughout the game to complete many objectives. -1- The first Great Fairy is located at the peek of Death Mountain. There is a wall that is made up of stone. Just simply use a bomb to reveal the entrance. Walk in and play "Zelda's Lullaby" on the triforce symbol to awaken the fairy. This fairy will give you magic power and a new charged spin attack. When pressing and holding the B button down, Link is charging up his sword to unleash a greater attack. Each charged up sword attack uses magic power.
-2- The second Great Fairy Fountain is located on the road to Hyrule Castle. After passing through the market, climb up the vines that are on the right side of the path. After reaching the top keep walking and jump to the other side of the gate. Follow the path until you reach a sign. Keep going and behind the sign there should be a big boulder. Blow it up with a bomb to reveal the entrance. Go in and play "Zelda's Lullaby" to awaken the fairy. This fairy gives you the magic spell, Din's Fire. It will come in use later on in the game.
-3- The third Great Fairy Fountain is located in Zora's Fountain. Behind and to the right of Jabu-Jabu, there is a small patch of land. Jump into the water and swim over there. There are several boulders against the wall. Place a bomb next to one of them and the whole wall will crumble revealing the entrance. Go in, play "Zelda's Lullaby" and you will get, Farore's Wind. This magic spell allows you to use warp points in dungeons. This weapon isn't necessary but can save time.
-4- The fourth Great Fairy Fountain is located in Death Moutain Crater. You can't go to this fountain until you beat the Fire Temple. Once you enter Death Mountain Crater from the secret entrance in Goron City, go right. There should be boulders there. Use the Megaton Hammer to break the boulders revealing the entrance. Go in, play "Zelda's Lullaby" and the fairy will double the amount of Magic Power you will have.
-5- The fifth Great Fairy Foutain is located in the Desert Colossus. Once you enter the Desert Colossus go along the right side. There are two palm trees. In between there is a small crack, bomb the crack and go in. Play "Zelda's Lullaby" to awaken the fairy. The fairy will give you the magic spell, Nayru's Love. When you use Nayru's Love you make a protective bubble around yourself that protects you from enemies and other things.
-6- The sixth Great Fairy Fountain is located right near the entrance to Ganon's Tower. The entrance is to the right of the entrance to Ganon's Tower. Using the golden gauntlets move the huge rock that is blocking the entrance to the fairy fountain. Go in, play "Zelda's Lullaby" and awaken the fairy. The Great Fairy doubles your defense. Enemy attacks will now be only half as effective.
Regular Fairy Fountains-Regular Fairy Fountains are located throughout Hyrule. They are filled with fairy spirits that fill up your hearts. You can also use your bottles to capture them for future use. -1- The first Fairy Fountain is located in the Sacred Forest Meadow. At the end of the maze you will get to some stairs that will lead to the Forest Temple. Before going up the stairs you can turn around and see a ladder. Go up the ladder and walk forward you will find a square pit. Fall down and you will see a small hole in the ground. Go in and collect a few fairies.
-2- The second Fairy Fountain is located in the Graveyard. In the first row of tombstones, one of the tombstones is marked with plants. Pull the tombstone back and fall in the little square that is revealed. There is a wall that looks a little different. Bomb the wall and enter the fairy fountain.
-3- The third Fairy Fountain is located in Hyrule Field. The Fairy Fountain is to the left of the drawbridge that enters into the Market. It is near a Peahat(the orange/red things that fly around Hyrule Field). Near to the peahat is a lonely boulder. Bomb it and it will reveal a hole. Jump in and get the fairies.
-4- The fourth Fairy Fountain is located in Zora's River. It's in a very hard to find place. The river flows toward the entrance to Zora's River. As you are near the end of Zora's River and are in the water you start flowing back to the entrance of Zora's River. As you flow you will reach a point where you can either go straight or go to the right. Go straight and you will see a small patch of land on the right side and you will see a ladder on it. After you get back to land, bring a chicken to the area where the river splits and jump with the chicken to the small patch of land. Climb up the ladder and you will find an area with a circle of rocks. Place a bomb in the center of the rocks to reveal a hole. Jump in it and get the fairies.
-5- The fifth Fairy Fountain is located in Gerudo's Fortress. When the Gerudo Thieves imprison you when you are an adult, using the Stone of Agony you can find where the hidden hole is located.
-6- The sixth and final Fairy Fountain is located in the Desert Colossus. There is a small dried up area where a pond should be. If you stand on it and play the "Song of Storms" the pond will fill with with water and fairies will appear.