Water Temple:
Drop into the water and swim along the right wall to a ledge. Then equip your Iron Boots and drop down to the bottom. Find the tunnel with the torches on either side of it and go in there to meet Ruto. Walk to the center of the room after she leaves and take off your Iron Boots to float up. Play Zelda's Lullaby in front of the Triforce symbol that's there and the water level will lower. Go through the door that's there to get your dungeon map. Drop down and you'll be in a room with two unlit torches and a lit one. Light the torches by shooting arrows through the lit torch or use Din's Fire. Go in there and kill the clam guys. Z target a clam and hold down your hookshot button to aim at it, then walk up to it until it opens it's mouth and then release the button to fire the hookshot. Kill them this way because in a bit you're going to have no choice but to kill clam guys with your hookshot. Now go back into the main room.Follow the left wall, skip the next tunnel and go on to the tunnel after that with the block in front of it. Push the block all the way forward and it will drop down. Jump down and go down the passageway then up the other side. Now hit the shock switch (the thing that looks like a diamond) and jump onto the geyser that shoots up then jump over to the other side. If you fall down there's a hookshot target you can use to get back up. Now you'll be in a room with a big whirlpool. Equip your Iron boots to sink down. Go stand on the piping under the water across from the stone head. Aim your hookshot to hit the crystal shock switch in it's mouth, then turn and fire the hookshot at the hookshot target inside the underwater passage. Go down the passage and float up and grab the key, then hit the shock switch that's in there to reopen the gate and use your Iron Boots to walk back out. Take off the boots and float back out of the whirlpool and make your way back to the main room. You'll need to use the hookshot to get out of the hole at the end of the tunnel. Stand on the block you dropped down then look up and you'll see a hookshot target you can use.You should have 2 keys now. Go to the tower in the middle of the main room and find the locked door and go through it. Use your hook shot to go up to the ledge above you then play Zelda's Lullaby in front of the Triforce symbol to raise the water level. Now put on your Iron Boots and drop back down. Underneath where the block was is now a hole. Drop down and follow this corridor and you'll end up in a room with a shock switch. Hit it with your hookshot from a distance and back away as a bunch of baddies drop down from the ceiling. Here's a battle tip for you. Z target the rock thing (the thing that turns into a spiked ball when you get to close) and hit it with your hookshot to kill it and it won't even be able to attack you. If it does come at you, block it with your shield and it will turn back into a rock thing. Walk around Z targeting all the rock things and kill them and you'll be left with two clams. Kill them using the hookshot method you used before. Once they are all dead a grate on the other side of the room will open in the ceiling. Float up there to get another key. Go back to the tower room and go through the upper door.Walk around until you see a tunnel with two pots in front of it and go in there. Follow the passage, use your hookshot to get over the spikes, then use your hookshot again on the ceiling to get up in the room. Go stand next to the treasure chest and shoot an arrow at the shock switch. Then get the compass. Go back out to the main room. Jump in the water, put on your boots, and sink to the bottom. Walk into the room where you met Ruto (the one with the torches on either side of the entrance) and float up. Blow open the crack in the wall to get your third key. Now go back into the main room, unequip your boots and swim left across the wall. Enter the first locked door you see. Go stand on the water geyser and then shoot an arrow at the shock switch to have it shoot you up to the next room (you can also use a bomb if you are out of arrows). Go through the door and you're at the high water level Triforce mark. Play Zelda' Lullaby to raise the water level to it's highest point. Now drop into the water and swim left to a locked door and go through it. Hop down two platforms and this platform will move. When it's at it's lowest point jump to the non-moving platform to your right. Now use your hookshot on the hookshot targets on the fronts of the moving platforms to make your way up to the top of the waterfall and go through the locked door. Now your in the water level puzzle room. If you mess up at any part of this room and fall in and the water level is low, use your iron boots to sink to the bottom then use the hookshot to hit the shock switch and raise the water level, then float up and climb back on to the starting platform to start over.Use your hookshot on the shock switch in the middle of the room to raise the water, then hookshot over to the statue nearest you. Now shoot the switch again with the hookshot and the water will lower. Walk to the back corner of this platform and look to your right. Use the hookshot on the hookshot target on the wall to get over to the next platform. Climb over the statue head and walk to the edge and shoot the switch again to raise the water again. Now hookshot to the next statue and hit the switch once again to lower the water. Now stand on top of the statue's head and shoot the switch a final time to be taken up to the next level. Kill the annoying spider things and kill the Shield-eater with arrows then use the hookshot target in the ceiling to get over the spikes. Go through the door and you'll find yourself at a big lake with a dead tree in the middle and a pillar on the opposite side. The lake is an illusion. Just walk over it and walk up to the pillar on the other side. You can't get in the door, so turn around and you'll come face to face with...yourself! In the form of Dark Link. Okay, this guy may seem impossible but there's a trick that makes him easy to beat. First, stand on the island in the center of the lake and make sure he stands on it too. For some reason, if he's standing on the island he won't attack nearly as well. Some say it has something to do with the lack of a reflection. You can also use the islands to either side but there's a glitch in the game that sometimes causes him to be stuck in the wall and you can't get him, so use the middle island. Anyway, once you've done that try hitting him with your hammer. If he blocks, take out your sword and hit him once with a regular swing (NOT a stab) and he'll deflect it but then be vulnerable, so take out your hammer again and it should hit this time. Then just keep smacking him with the hammer while staying on that island and he'll go down in no time. If you can't get this to work use Din's Fire.Now the lake will disappear and reveal where you really were...just a large room. Go through the now unblocked door and get your nice new shiny Longshot. Now look behind the chest and there's a temple of time block. Get rid of it with the Song of Time and drop down the hole. You'll be at the mouth of a river. Swim down river and when you start coming close to a whirlpool, use your Iron Boots to wade past it. If you get caught in it's pull and can't get out, try to get as far away from it is possible and then take off the Iron Boots and start tapping your B button like mad to swim away from it. Make your way to a small platform on the left side of the river, just before a particularly strong whirlpool. Use an arrow to shoot the gold eye across from you and a grate will open with a treasure box behind it. Use your hookshot on the treasure box to fly across, avoiding the last 2 whirlpools, and open the box to get a key. Go down the hallway and you're back at that whirlpool you got a key from earlier. Now make your way back to the main room (you should know the way) and with your Iron Boots on go once again through the tunnel with the torches on either side where you met Ruto, and float up to the water level changing switch. Play Zelda's Lullaby to change the water level, then drop down and go back into the main room.Go into the tower and play Zelda's Lullaby there to raise the water to the middle level. Exit the door and go around the tower to the back. There's a tunnel here with a grate and a gold eye below the entry. Shoot the gold eye with an arrow then quickly use your Hookshot on the Hookshot target at the end of the hall. Follow the passage until you hit a movable block. Push it forward out of your way, turn left and get the key. Now go back the other way and use your hookshot to fly up the hole in the ceiling and go down the hall to drop down back into the main room again. Sink down to the bottom and go into the passage to the right of the passage leading to the room where you met Ruto. Float up the other side. Use your hookshot to get over the spikes and go through the locked door.In this room kill as many of those spider things as you can first then use your Iron Boots to wade through the middle of the water, avoiding the whirlpools and the boulder. Float up and out on the other side and go through the door. Drop to the nearest ledge on your right and blow open the crack in the wall. Don't go through it yet. Instead, swim across to the left platform and blow open the discolored bricks. Go through this one and push that block that's in there all the way forward. Now loop back around to the first hole and go in there and pull the block as far as you can. Loop back around once again and push it the rest of the way onto the underwater switch. This will raise the water level. Float up with it and go through the door (not the one you came through, the other one. It's got steps in front of it). Now in this room step on the floor switch and quickly cross the gap by hopping on the water geysers then go through the door. You don't have to jump on the third geyser, you can make the jump from the second to the door to save time.In here avoid the boulder and head right (upstream) then use your boots to sink into the deep water. Walk along the passage, float up the other side and go through the locked door. Get the Boss key from the treasure chest. Now go back outside, go down stream and you're back in that room with all the spider things and the vortex's. Go back through the door you first came in and make your way back to the main room again. Once there float up and go through the door with the red block floating in front of it and raise the water to the highest level. Now look for one of those dragon head statues with a hookshot target on it. Use the hookshot to get over there and go through the door behind it. Go up the ramp while trying to avoid those moving spike things (this is a lot harder than it sounds. Try going up the right side when the first spike thing is moving to the left and about halfway over and keep running straight up) and go through the boss door. Jump onto one of the platforms and you'll get a warning about the water. Now you'll meet...
Water Temple Boss: Morhpa
This boss is fairly tough but not overly so. When it start to morph into a tentacle just get far away from it. You can use your hookshot on the targets on the walls to get away faster. I stayed on the outside edge all the time so as to avoid falling in the water. Now once you're far enough away Z target that little red thing and when it stops spinning around so much, use your hookshot to pull it out of the tentacle and bring it toward you. Then hit it with your sword. Another method is using your Din's Fire spell. Stay fairly close to the tentacle that has the little red thing in it. When it's about to grab you use Din's Fire and the tentacle will dissolve. Then quickly do a Jump attack (push A) on the red thing to get in a nice solid hit. Another idea is to try to corner the red thing and just wail on it not letting it get back into the water. After a bit it will start using two tentacles which is more difficult. If one of the tentacles gets you you're in for some serious damage. Just keep doing either or both of these methods and that little red thing will finally die. The water will drain so go nab your heart container and step in the blue light and you're finally past this hellish level.
Kakariko Village in trouble:
After the short story sequence look around on the island you are standing on and find a plaque that talks about shooting into the morning sun. Use the Song of the Sun to make it night, then wait until dawn and shoot an arrow into the rising sun. A fire arrow will drop down onto the island across the water from you. Go get it. Now go to Kakariko Village using whatever method you like and as you walk in, you'll see...we'll I'll let you see for yourself. Sheik will teach you the Nocturne of Shadow here. Use it to warp to the entrance of the Shadow Temple. Go in the cave behind you and you'll see a ton of unlit torches. Stand on the platform in the middle and use Din's Fire to light all the torches simultaneously and open the gate to the Shadow Temple.
Bottom of the Well:
The entrance to the bottom of the well is in the Past area of the game. You will have to return from the Temple of time, go to Kakariko, enter the Windmill and play the song of storms there. Then the water will unflow from the well and you will have access. This level is nasty. So, after 2 hours of mapping it out, I've found a way to get to the Lens of Truth very quickly. There are a bunch of treasures scattered in this level but they are almost all WORTHLESS! Most of them are a single Deku nut. I'm going to tell you how to get the Lens of Truth, a gold rupee (worth 200 rupees), and finally the 3 gold skulltula's that are here (I've never mentioned most of the gold skulltulas before but explaining them here instead of making you explore this whole confusing level to get them is just easier.) Crawl through the hole and climb down the ladder. Kill the skulltula then walk straight forward right through the wall in front of you (yes, you heard right, this level has walls you can walk through, invisible floors, etc.). Now you're in the main well room. Watch out for the giant green flaming skull flying around and just keep running straight forward through another wall. Now ignore everything in this room but watch out, there's a small invisible pit right in the center of the room where all that blood is. Move around the pit and keep moving forward to the opposite wall and, again, walk through it. Now stand on the Triforce symbol in front of you and play Zelda's Lullaby. The water will drain out.Now turn around and go back through the wall, avoid the pit, through the next wall, and you're back where you started, except now there's a big pit in front of you. Fall down it and crawl through the hole that's down there. Kill the skulltula, climb up the vines and go through the door to the Bottom of the Well boss. This guy is scary but easy. It's basically a swing-your-sword-wildly-at-anything-that-moves affair. You can kill the hands coming out of the ground. If they grab you just wildly mash your buttons until they let go and keep slashing at them. You don't need to kill the hands, just the weird thing walking around trying to bite you. Once it's dead, a treasure box will appear containing the Lens of Truth. Use the lens of truth in this room and you'll find an invisible treasure box. Open it for 200 rupees. Now if you wish, you can just leave now by playing the Prelude of Light and go on to the next section. Otherwise, read on for how to get the 3 gold skulltulas in this level.First, leave this room, climb through the hole and up the vines to get out of the pit. Now go down the left path a little bit and if you use your lens you'll see a small alcove in the right hand wall. Go in and retrieve the key that's there. Now leave the alcove and go left (back toward the starting point). Keep going and you'll hit a left turn. Turn and use your lens and you'll see another alcove containing another key. Now leave the alcove and continue down the corridor. A little ways more and you'll see a cage with a Shield-eater in it. Directly across from it is a wall you can walk through. Go through it and walk straight across the room (avoid the pit in the middle! You can see it with your lens now). Go through the opposite wall and down the small corridor. You'll see a grate ahead of you. Fall down the pit you come to, walk under the grate, and climb up the vines on the opposite side and go through the door.Now in this next room is a mummy. Use your Song of the Sun to stun it and kill it with your sword. Now take out a Deku stick and light it with the torch but DO NOT LIGHT ANY TORCHES with it yet. All these torches open the coffin next to them and will release more enemies. You need to light a specific torch. It's the torch in the corner furthest from the door and to the left when looking from the door. Light the torch and the coffin will open letting out two bats. Kill the bats and inside the coffin is the third and final small key. If the bats burned away your Deku shield don't worry you can get another free one on the way to the third spider. Now head out of this room, fall down the pit and climb up the other side, and go straight through the wall in front of you. Look left and there's a locked door. Go through and kill the plant, watch out for the pots, they attack you, and there's spider number 1.Leave and turn left, avoid the pit, and there's another locked door on the other side of the room. In here is a bunch of bats and a big pit in the middle. Don't worry, there's an invisible floor. Just walk around the outside of the pit and you won't fall in. The spider is in the opposite corner of the room from where you entered. Now leave the room, turn left immediately and walk through the wall. Turn left again and continue down this corridor. You'll see some kind of face picture on the wall at the end of the corridor. Right underneath it is a pit so don't fall down it. Now turn right at the end of the corridor and you'll be at a dead end with a hole to crawl through. Crawl through and go through the locked door. Before moving into this room use your lens to see all the pits spread all over the place. Kill the bats and kill the laser shooting thing in the middle of the room by throwing a bomb at it. The chest in this room contains a replacement Deku shield if you lost yours. Go through the door and you'll be in the cage with the Shield-eater. Avoid it when it tries to suck you into it and hit it with your boomerang or sword when it stops. Kill the third and final gold skulltula in this room. Now use your Ocarina and play the Prelude of Light to warp out of this hellhole and end up back in the Temple of Time. Go into the Master Sword room and replace the Master Sword to warp to the future and continue your main quest. Pat yourself on the back for getting 3 well-earned skulltulas and the Lens of Truth.
Shadow Temple:
If you haven't already gotten it, go back to the Quest for Truth section and get the Lens of Truth. You need it for this level. Go down the hall and turn the corner, use the hookshot to get across the pit, and you'll see a wall in front of you. Walk through it. Immediately turn left and follow the wall two face tiles down and walk through the wall again (use the Lens in any area to see where the walls can be walked through). Now go through the hall and door and go through another wall to come to a room that seems to have no exit (but we know better right?) As soon as you enter head right and follow the wall until you find an opening (use lens if you want). Go through the door behind it and then play the Song of the Sun to stun the zombie and kill it, then hunt down and kill the two bats. Get the chest that appears for the Dungeon Map.Now go back out and head right following the wall to an opening behind a walk-through wall with a pot on either side of it. Keep going down this tunnel and you'll end up in a room that looks the same as the last one. The opening to go through next is in the corner on the right with a pot beside it. Go through the door there and you'll face Dead Hand, which is the same guy that you killed to get the Lens of Truth in the bottom of the well. After this easy kill, a chest with the Hover Boots will appear. Snatch your prize then go all the way back through to the first big room that had the statue in the middle of it.Use your Lens and look at the skulls on the pillars around the circle, and see which one does NOT disappear with the lens. Now walk up to the tab sticking out of the side of the base of the statue and push the statue until the tab you are pushing is pointing toward the skull that didn't disappear. Don't stop pushing until it gets there or you'll fall in a pit. Now put on your hover boots and walk across the pit to the tongue-looking platform and go in the door and down the ramp. Kill the laser eye in the middle of the next room by throwing two bombs at it, then stand in the middle of the round platform it was on and play the Song of Storms for a Big Fairy (Big Faeries heal both life and magic but can NOT be captured into a bottle. Also note that all you have to do is leave the room and come back in and you can get it again.). Go through the wall on your right, kill the mummies (stun them with Song of Sun if need be) and get the chest containing the compass.Exit back to the eye laser room and go straight through the wall on the other side. You'll end up in a big room with two Deaths swinging giant scythes around the room (it's not enemies, it's just a giant statue). Avoiding the blades, grab all the silver rupees in the room. Note that one is on a platform that has a hookshot target on the wall above it, so use the hookshot to get to it. Now go through the alcove it opened and get the small key. Return to the eye laser room and use a bomb to blast open the remaining wall leading North. Go through the locked door. In this next passage watch for round small shadows on the ground. They are Skulltulas waiting to drop on you. Kill the three Skulltulas and drop down the ledge ahead and you'll be facing some dropping blades. Dodge the first blade, kill the Skulltula, then go past the second and keep following the tunnel. Now you'll be in a huge room. Take off the Hover boots if you're using them, otherwise you might slide into a blade. Jump over the pit, dodge the blade and jump over the next pit, dodge the second blade and jump over the pit, and just before the third blade watch out for a flaming skull to try to get you. Kill it then dodge the final blade.Now on this island you'll have to kill a Stalfos. Once he's dead, play the Song of Storms in the middle of the island for a Big Faerie. Put your Hover Boots on. Facing away from the last falling blade, turn left and use your lens to see an invisible platform. Hover on over it and the next platform, turn right, and hover on over to the door there. Go through and use your lens to see the big spinning scythes thing. Kill the Shield-eater and look on the walls to find 3 bats to kill. Kill them and the door will open. Go through it to kill a gold skulltula, open a chest for some rupees, and open the invisible chest using the lens for some arrows. (Yes, that was just for two stupid treasures and a gold skulltula but I didn't want people complaining that I'd missed some treasures). Now head back out and hover back to where the Stalfos was. You can use the Song of Storms for another Big Faerie now if you want.Wait until the platform in front of you falls and hover forward as far as you can go to land on it (it's farther than it looks). Then wait for it's highest point (you'll have to time it) and hover over to the next big island. Collect all the silver rupees here (there's on inside that eye laser thing so kill it) and go through the door that opens. Follow this passage to a room with falling spikes. Use your lens and look at the right hand wall to see a movable block. Pull it out onto the face tile and then push it in front of you and it will keep the spikes from hitting you. Once it's on the second face tile walk around and start pulling it until it's on the third face tile. The treasure box in the cage to the right has arrows. Climb up on to your block now and hover/hop to the ledge on your left. Now wait until the spiked platform lowers and walk over it to get to the platform on the other side of the room. The treasure box has rupees, but more importantly the yellow switch makes a new treasure box appear on the other side of the room. Hover there using the spike platform as before and get the small key. Leave this room back to the big room.Now look at the left hand corner of the platform you are on (the one furthest corner from you) and you'll see a small rock ramp. Use it to get to a platform with a falling blade. Use your lens to see the ledges behind the blade, then dodge and hover to the platforms and finally to the locked door on the wall. In this room use your lens to see the invisible spikes on the floor. Kill the two zombies and a rupee chest will appear. Now to get all the silver coins here, hookshot to the hookshot targets on the wall. To get the last one, use your lens to see an invisible hookshot target above an invisible platform. Hookshot up and hover walk off the platform to get it. Once you have them all a door will open, go through it. In this room kill all the bats to reopen the blocked door that shut behind you. Climb up the steps and pick a bomb plant then toss it into the hole in the top of the giant skull to blow it up and get the small key it drops. Go back into the last room. Use your lens and look on the ceiling above the raised platform for an invisible hookshot target. Use it to get on the platform and go through the locked door.Now I know this sounds weird but, put on your Iron Boots. This will keep the fans in the tunnel ahead from blowing you away. Make your way through the tunnel until you come to a pit. Watch the fan on the other side of the pit and as soon as it stops blowing, equip the hover boots, walk across, and then reequip the iron boots. Drop down off the ledge and walk across the bridge to the door. You can kill the eye above the door that's shooting fire at you by hitting it with an arrow while the eye is open. In this small room kill the two zombies to reopen the door, play the Song of the Sun (not storms) in the middle of the room for a Big Faerie, open the invisible chest for some arrows, use z-targeting and Navi on the face for a hint, then leave. Use your lens to see a hole in the right wall, then stand even with it. Look at the fan behind you and when it stops, turn around and equip the hover boots. Stand on the side of the bridge closest to the fan. Watch closely and when you start moving from the fan run across to the opening in the wall. The fan helps blow you across. Go through the door.As soon as you walk in this room, look to your right and there's a pile of dirt there. Blow it up with a bomb, then use your Lens to see the invisible chest containing a key. Kill the two mummies for another rupee chest and go through the locked door. Once you're through this door turn left and go to the movable block. Pull it onto the path of green bricks and then pull/push it onto the face tile under the ladder on the opposite side. Climb up onto it and go up the ladder. Hop over onto the ship, stand on the Triforce symbol, and play Zelda's Lullaby. As the ship moves you'll have to fight two Stalfos. When the ship completes it's journey, whether or not you're done with the Stalfos, it will start sinking. Jump off to the left (if you're facing the front of the ship) onto the platform there before it sinks. Go through the door that's on the platform.This next room has 4 doors at North, South, East and West (you came in the East door) and is a small maze of invisible walls. It's inhabited with those hand things like from the Forest Temple. Use your lens to navigate it. The West room contains three giant rotating skull heads that give you some rupees and a gold skulltula. The South room contains an invisible hand monster (use Lens of course) and a chest that appears once it's dead containing a small key. The North room contains two spiked walls that close in on you to kill you. Use Din's Fire to burn down the walls and recover the Boss Key and some rupees. Once you get the Boss Key and small key, return to the room where the ship dropped you off (through the East door).As soon as you're back in this room, look up and to your right to see a high platform. If you have the Scarecrow's Song you can play it to get Pierre to appear up there and then Longshot to him to get across. If not, go to the other end of the platform and look over to a large statue and some bomb plants. Shoot one of the bomb plants with an arrow to blow them up and make the statue fall over the gap creating a bridge. Once you're over go through the locked door. Use the Lens and Hover Boots to walk over the gaps and invisible platforms and go through the Boss Door. Make sure you're still wearing the Hover Boots and fall down the hole in the middle of the room to face...
Shadow Temple Boss: Bongo Bongo
This boss is easy if you know how to do it. Stand far away from the hands. Z-target one of them and fire off a regular arrow. It will turn blue. Then Z-Target the other and hit it with an arrow. Now as soon as it also turns blue, turn on your Lens and, push B once to take out your sword, then hold down B to start a spin slash charging. Wait until Bongo Bongo's eye is close enough and let the spin go. Start slashing it with the sword until it retreats. Then repeat until he dies. With the Big Goron's sword he should die fairly quickly. Grab the Heart Container and step into the blue light to get out of this tricky dungeon.
Young Link
Forest Temple through Ice Cavern
Spirit Temple through End Game