Stray Fairies
This section describes in detail where to find the shattered Great Fairy pieces in Clock Town and the four temples as well as where to find the fountains to receive your rewards.

Clock Town

 

#1 (Day)

 - During the day, the Stray Fairy can be found in the Laundry Pool, floating above the water.

#1 (Night)

 - During the night, the Stray Fairy can be found in the East Clock Town, floating in the middle of the square. Use the nearby flower to launch yourself to get it, or just put on the Great Fairy Mask.
 

Fairy Fountain
Location

 - The Clock Town fountain is hiding in the corner of North Clock Town. It's pretty obvious as well as imperative to your quest.

 - The Great Fairy of Magic rewards you with the ability to use Magic, which allows you to use Bubble Blast in your Deku Form and charge up your Spin Attack a little.

Reward:
Magic (Bubble Blast)

 

Woodfall

 
 - ENTRANCE Room.
#1
 - As soon as you enter, use the Great Fairy Mask if you have it.
#2
 - Open the chest on the second platform.
 
 - MAIN ROOM with the GIANT SPINNING FLOWER.
 - Without Hero's Bow.
#3
 - Kill the Deku Baba at the end of the wooden ramp.
#4
 - There's a little island in the corner with several pots filled with goodies. In one of them is a Stray Fairy.
 
 - Room with the FLOWER in the center and the FOUR VENUS FLY TRAPS surrounding it.
#5
 - On the platform where the small key is, turn to your left to bee hive against the wall. Hit it with a Bubble Blast or two to knock it down, then snag the Stray Fairy by spinning into it with the Deku Mask or use the Great Fairy Mask.
 
 - Room with the skinny walkway, STONE BLOCK, and TORCHES.
 - Without Hero's Bow.
#6
 - Kill the Skulltula.
 
 - DARK room.
#7
 - Kill all the Black Boes to make a chest appear.
 
 - MAIN ROOM with the GIANT SPINNING FLOWER.
 - When you return WITH Hero's Bow.
#8
 - On the top level of the Main Room, there's a Stray Fairy just floating there, trapped in a bubble.
#9
 - Next, put on the Deku Mask and use the flower here to get to the little platform in the northwest corner of the room with the unlit torch. Take off the Deku Mask and step on the switch.

 - This will cause a chest to appear near the beginning, make your way over there and open it.
 
 - Room with the skinny walkway, STONE BLOCK, and TORCHES.
 - When you return WITH Hero's Bow.
#10
 - Kill the Deku Baba at the end of the wooden ramp.
#11
 - There's a little island in the corner with several pots filled with goodies. In one of them is a Stray Fairy.
 
 - Room right BEFORE THE BOSS with all the CUBBIES and DEKU FLOWERS.
#12
 - Trapped in a bubble in one of the cubbies on the right side.
#13
 - Trapped in a bubble in one of the cubbies on the right side.
#14
 - Trapped in a bubble in one of the cubbies on the left side.
#15
 - This one is floating on the left side of the room, in one of the pillars ahead of you. Shoot the bubble to release the last Stray Fairy, and use the Great Fairy Mask to reel it in.
 

Fairy Fountain
Location

 - The Woodfall Fairy Fountain is in the cliff behind the Owl Statue. Fly over to the nearby flower and use it to get there.

 - The Great Fairy of Power rewards you with a stronger Spin Attack.

Reward:
Magic (Bubble Blast)

 

Snowhead

 
 - Room with the THREE FREEZARDS (icy breath and the PARTIAL BRIDGE you have to GORON ROLL across near the beginning of the temple.
#1
 - This one is trapped in a bubble within the pillar holding up the second half of the bridge. It's easier to see from down below.
#2
 - The second Stray Fairy is in a bubble under the ledge leading to the stairs on the far side of the room. Shoot it and use the Great Fairy Mask.
 
 - Room with the ICE COVERED PILLARS where you shoot the GIANT ICE SICKLES to break them.
#3
 - Climb onto the first three little pillars. Straight ahead, in the wall, you'll notice an icy patch that looks funny.

 - Use the Lens of Truth if you like to see that it's a hidden cubby in the wall. Jump in and open the chest to snag your prize.
 
 - Room with the GORON SWITCHES.
#4
 - Kill the White Boes here and stand near the center of the snowy area below. Look up while wearing the Great Fairy Mask and using the Lens of Truth. Shoot the center of the dark area to pop a bubble.
 
 - Lowest level of the MAIN ROOM, the Basement.
#5
 - You'll find a large switch in the lava. Wear the Goron Mask and step on it to cause a chest to appear in another lava puddle. Snag it, then head back up the stairs.
 
 - Room with LOTS OF SMALL PLATFORMS, THREE FREEZARDS (icy breath enemies) and THREE TORCHES.
#6
 - Kill the three Freezards in this room to make a chest appear.
 
 - Room with the WHITE WOLFOS and FROZEN STUFF. Also the room with the TWO BLOCKS, one on top of the other.
#7
 - In this room, right near the cracked wall we blew up earlier to reveal the stairs is a crate atop one of the pillars.

 - Throw a Bomb at it to blow it up, then use the Great Fairy Mask to reel it in.
#8
 - Right next to you is a frozen switch. Melt it, kill the White Wolfos, then step on the switch to make a chest appear on a ledge.

 - Melt the nearby frozen block. Now, if you look at it from your MAP PERSPECTIVE, push the block UP, RIGHT, then  DOWN.

 - Jump onto the ledge and open the chest.
#9
 - If you moved the "double blocks" in an earlier room into a little slot, there is another Stray Fairy you can get now.

 - Push the block LEFT, UP, LEFT. Jump onto the second platform and enter the door.

 - In this familiar room, if you placed the double blocks in the right place (where it fell into a slot), you can use them to jump to the other side. Open the chest when you get there to claim your prize.
 
 - FROZEN EYE SWITCH/ELEVATOR room.
#10
 - As you come up the stairs, this one is directly on your right, just floating there.
#11
 - In the upper level of this room, use your Lens of Truth to see tiny hidden platforms. Use them to reach a cubby above the stairs with a hidden chest containing another Stray Fairy.
 
 - Room with several EENOS (snow monsters).
#12
 - In the south portion of this room are three blue stalactites in front of a little invisible cubby that's pretty obvious due to the snow hanging from its ledge. Use the Lens of Truth, Great Fairy Mask and Hero's Bow to pop the bubble hidden in the center.
 
 - Room with the two DINOFOLS (fire breathing lizard swordsman).
#13
 - Kill the first Dinofol.
#14
 - Kill the second.
 
 - On the SECOND FLOOR of the MAIN ROOM.
#15
 - In the main room, there is a small hidden cubby that holds a chest containing the last Stray Fairy. You can see where it is by the patch of ice hanging off the ledge (or use your Lens of Truth).

 - To get to it, you'll have to jump from a higher level, by
using the Goron Mask, Bunny Hood or Deku Mask to roll, jump, spin or fly (using the flower on the top floor) towards it. If you're lucky, you'll land in there.

 - The best way in my opinion is to stand on top of the pillar in the center of the room after you've punched out the ice cylinders, and spin towards the cubby with the Deku Mask. You will just make it, no problem.

 - Once you get it, you can salvage some ascending by using the flower there to fly to the third floor on your left.
 

Fairy Fountain
Location

 - The fairy fountain is located at the base of Snowhead around the side.

 - The Great Fairy of Wisdom will double the size of your Magic Meter.

Reward:
Magic Meter

 

Great Bay

 
 - The ENTRANCE ROOM.
#1
 - There are four unlit torches near the first door. Either shoot them all with Fire Arrows or run along them with a Deku Stick (there's some in the barrels nearby). If you light all of them in time, a chest appears.
 
 - Room right after the entrance room where you CHANGE THE WATER DIRECTION for the main room.
#2
 - The next one is trapped in a bubble underneath the platform you enter this room from. Sink down with the Zora Mask and grab it.
#3
 - There are two platforms rising up out of the water repeatedly. Take the right one (when facing the door) to come to a platform with Rupees and a Skulltula. Kill it to find the Stray Fairy.
 
 - MAIN ROOM with the SPINNING WATER.
#4
 - On one side of the room, there's a barrel atop one of the small platforms with the ladders. Break it and snag the Stray Fairy.
#5
 - There's a lone jar in the center of this room in the 'eye of the storm' of spinning water at the bottom. Stand on the side and shoot an arrow at it, then wear the Great Fairy Mask. Or, just sink down and hit it with your Zora Fins, then try to swim into it.
 
 - TINY ROOM before the Boss Key room with all the BIO DEKU BABAS.
#6
 - Kill all the Bio Deku Babas to make a chest appear on the small ledge. Use the lily pads to get there.
 
 - Room with the BOSS KEY and COMPASS. It has water in the middle with a SMALL KEY in a chest at the bottom.
#7
 - On the left side of the flowing water (when you're facing the door), there are two Dexihands attached to the wall. Between them is a jar. Break it and use the Great Fairy Mask or swim into it.
 
 - Room where you find the MAP. It has some SKULLFISH and DEXIHANDS in it.
#8
 - There's a small platform with two pots on it. Break the pots to find a Stray Fairy in one of them.
 
 - Room with LOTS OF WATER and the YELLOW and GREEN platforms. This room has two BLUE TEKTITES (spiders) in it.
#9
 - Get to the YELLOW platform and face the wall opposite the door. If you look up, you'll notice some metal grating separating you from a small area up there.
 - In front (above) of you is a hole in the grating with a target nearby on the ceiling. Use your Ice Arrows to create platforms and get near the far wall, then turn around and Hookshot the target.
 - It may take a couple tries, but once you get up there, in the center you'll find a chest.
 
 - Room with the SPINNING WATERWHEEL that you can use FIRE AND ICE ARROWS to start and stop from turning.
#10
 - After you've used the elevator thing to go up, jumped onto the spinning waterwheel and are standing on the next moving platform, turn right and you'll notice a torch burning in a hole in the wall.
 - Use your Hookshot on it to find a small space with a chest.
#11
 - When you've frozen the waterwheel in this room, walk part way across the paddles, then turn right. When you get to the six blades (only two are accessible, pointing in either diagonal direction) climb onto the one on your right.
 - Climb to the end of it. You'll notice that straight ahead is a small hole in the wall with a chest. Hookshot the chest and open it.
 
 - Room with all the SEE-SAWS you use to lift yourself up.
#12
 - The first see-saw you come to when you enter the room, jump into the water on either side, sink down and break the barrel.
#13
 - When standing on the GREEN platform with the switch, kill the Real Bombchu, then walk along the GREEN pipes. Put on the Zora Mask and climb your way right.
 - Follow it and jump down into the small area when you can't go any further. Use your Hookshot on the chest and open it.
 
 - Room right BEFORE THE BOSS.
#14
 - At the exit to this room, there is a Stray Fairy in a bubble in the opening. Use your charged up fins to break the bubble, then swim into it.
#15
 - Directly underneath the GREEN platform is a Stray Fairy in a bubble. It's too high to get when you're in the water, so stand on the GREEN pipe right on the edge of the water and shoot it with an Arrow, then use the Great Fairy Mask.
 

Fairy Fountain
Location

 - The fairy fountain is located on the south side of Zora Cape, along the cliffs. To get there, jump along the stone platforms near the beach and then Hookshot your way across the islands using the trees. At the end, you'll need to use a bombS on the boulder.

 - The Great Fairy of Courage will increase your defense, making you take half damage from everything!

Reward:
Defense

 

Stone Tower

 
 Both:
 - ENTRANCE room.
#1
 - To get the first Stray Fairy, shoot the golden eye switch in one of the eyes in the giant figure straight ahead. Jump to the chest that appears using the Bunny Hood or Zora Mask. Open the chest. If you don't have that mask, you can get it later when you come through that door.
#9
 - Stand near the Majora's Mask emblem in the center of the room and turn around. Shoot a Light Arrow practically straight up into the Sun Face above you. Open the chest that appears next to you.
#13.1
 - Step on the switch with the Death Armos to make a chest appear on the ceiling.
#13.2
 - Head back to the entrance room and jump down into the pit deal and open the chest we created (that you need to Hookshot to, to get to the Boss room when the temple's upside-down).
 
 Right-side-up:
 - DARK ROOM with the FOUR ARMOS STATUES.

 Up-side-down:
 - Room where you battle the WIZROBE with LAVA DRIPPING FROM THE CEILING.
#2
 - There's a target on the ceiling that allows you to get onto a small, hard to see ledge. Find it and get up there. Open the chest.
#12
 - Open the chest after defeating Wizrobe.
 
 Right-side-up:
 - Room with LOTS OF WATER and a BRIDGE. LIGHT SHINING from the ceiling.

 Up-side-down:
 - Room with the DEKU FLOWERS and the AIR RISING from the holes in ceiling/floor. Also a BRIDGE with a MASKED HIPLOOP.
#3.1
 - This is a two parter. Sink down to the bottom here and charge up your Zora Fins to make the mines blow up. Step on the switch to make a chest appear for later. Don't forget!
#3.2
 - There's a small platform at the top of the room with a flame on it. If you stepped on a switch in this room (that was filled with water before) earlier, there's a chest here now.
 - Go to the small platform on the right side of the room with a switch on it. Play the Elegy of Emptiness to keep it down, then fly up and claim your prize.
#10
 - Right underneath the platform with the flower you start at, there's a Frozen Eye Switch. Jump down and shoot it with a Fire Arrow. This will make a chest appear on a nearby ledge. Use the middle air pump thing to get there.
#11.1
 - At the edge of the platform mentioned above, there's a Sun Face that can be shot from below that will make a chest appear. It's right-side up though, so you'll need to come back for it later.
#11.2
 - Go to the room with the all the water. On top of the platform at the bottom, there's a chest for the Sun Face nearby that you shot earlier.
 
 Right-side-up:
 - Room with all the MIRRORS, SUN BLOCKS and BLACK BOES (black fuzzy enemies that keep appearing).
#4
 - There are six Sun Faces on the wall near the light source. Use the far left one on the right side to make a chest appear.
#5
 - When standing in the light facing the pillar in the center of the room, charge up the mirror on the right. Now run over and use it to make the Sun Block on your right disappear. This will reveal a small area with a Nejiron and a chest.
 
 Right-side-up:
 - Room with AIR PUMP things and LAVA BELOW. SHAPED LIKE A "U".
#6
 - There is a chest on the other side that is surrounded by fire. Down below, there is a switch you can stop on as a Goron to put the fire out, but it's on fire as well.
 - Use a Goron Stomp (A + B) on the Goron Switch on the first side, then run and roll to the other side and step on the switch before the fire returns. This will put out both flames.
 - When you get to the other side later, open the chest.
#7
 - As you just start flying around the "U" shape, right before you turn the corner, there's a platform on your left with lots of Rupees. Go there and open the chest.
 
 Both:
 - Room with the WATER, MINES, SUN BLOCKS and a BRIDGE through the middle with an EYEGORE.
#8
 - Kill the Eyegore to make a chest appear.
#14
 - Go back to the room with the water, the bridge and the hand enemy. Use it to throw you up onto the ledge. Use a Bomb or a Spin Attack to hit the crystal switch to make a chest appear in the other area.
 - Go to the other side by either going back through the various
rooms, using a dolphin jump with the Zora Mask to get back on
the ledge, or play the Song of Soaring to get back to the start
of the temple and go through the two doors on your left. The
last way gets my vote for the best.
 - Use a Light Arrow to remove the Sun Block. Kill the Beamos
using a Bomb and open the chest.
 
 Both:
 - SKINNY ROOM right BEFORE THE BOSS DOOR with the MASKED HIPLOOP and SPIKED LOGS.
#15.1
 - Hit the crystal switch while the temple is upside-down.
#15.2
 - Go to the room with all the mirrors and Black Boes we had to tackle earlier. Follow this whole chain of rooms until you get to the room with the skinny bridge and the Hiploop.
 - Fall to the bottom and open the chest we created earlier.
 

Fairy Fountain
Location

 - The fairy fountain is located inside a little hut in Ikana Canyon near the entrance to Stone Tower.

 - The Great Fairy of Kindness will give you the Great Fairy Sword. Although it's a (C) Button item, it can be used as a weapon, four times as powerful as your original Kokiri Sword!

Reward:
Great Fairy Sword