Note: It is a lot easier to get all the fairies if you wear the Fairy Mask, because the fairies will come right to you.

Woodfall Temple
1. Right in front of you at the entrance. You can't miss it. (1st floor)
2. After using the Deku Flowers twice, you should be on a platform with a treasure chest. Open it. (1st floor)
3. In the near right corner of the next room. (1st floor)
4. Using a switch at the far left side of this room makes a treasure chest appear. Open it. (1st floor)
5. Defeat the Deku Baba in front of the door on the left. (1st floor)
6. On the ledge above the rest of the room there is a fairy hovering around a Deku Flower. (1st floor)
7. In the room to the right, shoot a beehive left of the door at the left side of the room. (1st floor)
8. Left of the room with the big wooden flower is a room with water and narrow walkways. At the back right corner, defeat the Skulltula. (1st floor)
9. Shoot a beehive beneath the first platform. (1st floor)
10. After you've purified the water, look around under the platforms for a fairy in a bubble. (1st floor)
11. In the dark room, defeat all the Black Boes for a treasure chest to appear. (2nd floor)
12. In the room just before the boss', use the Deku Flowers to find a fairy near the top left of the room. (1st floor)
13. Hit the crystal switch to make the fires disappear to reveal a fairy trapped in a bubble. (1st floor)
14. Use the Deku Flower to find a fairy on the right side of the room.
15. Use the next Deku Flower to find a fairy just above you.
Reward: Spin Attack
Location: If you're facing Woodfall from the Deku Altar, use the Deku Flower to fly into a cave behind and to the right of you.

Snowhead Temple
1. In the room where you have to jump from one end of a broken bridge to the other - under the first half. (1st floor)
2. In the same room under the doorway leading upstairs. (1st floor)
3. The first left turn you can make in this temple takes you to a room with a block you can push across ice. Push it straight, right, right, and open the treasure chest on the ledge. (1st floor)
4. From here, push the block left, right, left, left, right, right, and jump to the box. Turn into Darmani, and pound the box. (1st floor)
5. Use the block to get onto the ledge and to the next room. Find the block in this room, and push it to the other end of the room so that a treasure chest appears. Open it. (1st floor)
6. In a room with lots of platforms to jump to, defeat the three Freezards. (1st floor)
7. Jump to the very bottom of the main room, and step on the switch in one of the lava pits. Open the treasure chest that appears. (Basement)
8. From the room with the broken bridge, go upstairs. To the right of you is a fairy. (2nd floor)
9. In the same room, use the Lens of Truth to see an invisible path to a treasure chest. (2nd floor)
10. In the room south of the main room, use the Lens of Truth to see a fairy in the ceiling. (2nd floor)
11. In the room next to this one, use the Lens of Truth to see a hidden treasure chest in the wall with ice on it. (2nd floor)
12. In the room west of the main room, look where there is ice on the wall using the Lens of Truth. (3rd floor)
13. Defeat a Dinalfos. (4th floor)
14. Defeat a Dinalfos. (4th floor)
15. Using the Deku Flower in front of Goht's room, fly down while looking for a patch of ice on the north-western part of the wall. There is an invisible wall that you can go through here. (2nd floor)
Reward: Double magic power
Location: At the base of the right side of Snowhead Temple.

Great Bay Temple
1. Light all the torches in the first room. (1st floor)
2. In the next room, take the left elevator up and defeat the Skulltula. (1st floor)
3. Underneath the platform in front of the door. (1st floor)4. Break a barrel in the next room. (1st floor)
5. Jump into the water and take the near right passage. It's in a jar in the next room. (1st floor)
6. Follow the next passage and defeat all the Bio Deku Babas. (1st floor)
7. Sink to the bottom of the spinning water room. Break the pot. (Basement 2)
8. Freeze the waterfall blocking the ladder, and in the next room use the hookshot to reach a barrel on the yellow ledge. Look for a hole in the ceiling, and freeze some water so that you get a good shot at the target. (1st floor)9. In the spinning water room, take the far right exit and let one of the Dexihands throw you onto land. Break a pot underwater. (1st floor)
10. Keep following the passage and use the hookshot on a torch high up in the next room. Open the treasure chest. (1st floor)
11. After you've frozen the waterfall, cross the gears that used to spin and hook onto the treasure chest above them. (1st floor)
12. In the next room, unfreeze the ice above the seesaw nearest the door. Dive down and open the treasure chest. (Basement 1)
13. Use the other two seesaws to get as high as possible. At the end of the green pipe, jump over the fence. (1st floor)
14. In the room before Gyorg's, look in the passage that leaves his room (it's a one-way exit). (Basement 2)
15. Look under the switch before his room. (Basement 2)
Reward: Double health
Location: Swim to the left side of Great Bay Coast where there is nothing but a few islands. With the help of the hookshot, you'll reach a ledge with some boulders you can blow up.

Stone Tower Temple
1. When you first enter the temple, shoot the eye of the giant statue to make a treasure chest appear. (1st floor normal)
2. In the room where you find the map look for a target on the near right side and hit it with your hookshot. (1st floor normal)
3. In a room with six sun emblems near the door, shine a light on the far right one. (1st floor normal)
4. In the same room, use a mirror to make a blue block disappear. (1st floor normal)
5. In a room full of lava, use the Deku Flower to fly left around the first corner. (1st floor normal)
6. In the lava room, turn into Darmani and step on the switch in the lava. Carefully but quickly roll around the room to a switch that would otherwise be surrounded by flames. (1st floor normal)
7. After you defeat Eyegore a treasure chest will appear. (1st floor normal)
8. After you defeat Hiploop, drop off the ledge to either side. Look beneath the floor for a crystal switch and bomb it to make a treasure chest appear. (1st floor normal)
9. In the first room full of water, get onto the land at the far side. Place a bomb right next to the gate to hit the crystal switch to make a treasure chest appear. Swim back to the other side and use a Light Arrow to get rid of the blue block. (1st floor normal)
10. In the first room, shoot the sun emblem at the top with a Light Arrow to make a treasure chest appear. (1st floor flipped)
11. While the temple is in it's normal state, swim to the second room full of water. Step on the switch at the bottom. Turn the temple upside-down and go back to this room (it will have Deku Flowers and strong winds that lift you up). Fly to the right ledge, step on the switch and play the Elegy of Emptiness. Fly to the next highest ledge and open the treasure chest. (2nd floor flipped)
12. In the same room, use the middle wind to get under the exit. Shoot the frozen eye with a Fire Arrow to make a treasure chest appear. (2nd floor flipped)
13. Open the treasure chest after beating Wizrobe. (2nd floor flipped)
14. When the temple is upside-down, defeat the Dark Armos and step on the switch to make a treasure chest appear on the ceiling. Flip the temple, and re-enter it. The treasure chest will be at the bottom. (1st floor normal)
15. Open the treasure chest underwater in the second underwater room. (1st floor notmal)
Reward: The Great Fairy's Sword.
Location: A cave near the entrance to the Stone Tower.