After you obtain the Iron Boots in the Ice Cavern, you can reach the Water Temple in Lake Hylia.
This is one of the hardest temples in the game and has become infamous for its difficulty, but this guide will (hopefully) help you get through it much more easily. This temple has been made slightly less difficult in the 3DS version. The hardest part is making sure you don't miss any keys, because otherwise you have to do a lot of backtracking to find them. Just remember: if you get stuck, change the water level.
Reach the Temple
Go to Lake Hylia. The water is much lower than it used to be. Go into the small area of water in the center of the lake and put on the iron boots, then use the hookshot on the crystal to open the gate. Go in.
Get the Map
Once in the temple, take off the iron boots and float up to the ledge. Walk forward to the water, jump in and put the iron boots back on. If the Spike monsters approach you, use your shield or hookshot to make their spikes retract, hit them with the Hookshot to kill them.
Go through the path between two unlit torches. At the end, you find Princess Ruto, who is now all grown up. After she speaks to you, she will float up. Take off the Iron Boots to follow her. If you hit the ceiling, swim under the hole in the ceiling so you can go up the rest of the way.
Climb out of the water. Princess Ruto is not here. Go through the door and use your shield and Hookshot to kill the Spikes. Open the chest to get the map.
Lower the Water
Exit the room where you got the map, and go to the wall with the Triforce symbol on it. Take out your Ocarina. If you are standing in the right place (near the Triforce symbol), a musical staff will appear. Play Zelda's Lullaby. This will drain the water in the temple completely. Then fall down the hole in the floor. Normally you would get hurt from falling so far, but this is a special case where you will not get hurt.
Get a Key
In the room at the bottom, there are two unlit torches, and a lit torch in the middle of the room. If you don't have many arrows, break the pots in this room. Shoot an arrow through the flame of the lit torch, aiming at each unlit torch in turn. (Or you could use Din's Fire, but it uses up a lot of magic.) The door will open. Go through.
There are three shell blades here. To kill them, you have to hookshot the pink part inside the shell when it is open and facing you. If you don't do it in time, the shell will close, turn around, and attack you with its spikes. Kill the Shell Blades to make a chest appear. It contains a small key.
Get a Second Key
Exit and return to the big main room, which is now drained. One of the walls in this area has a large block in it. Climb onto the platform in front of the large block, and push the block forward until it falls into a hole ahead. Jump into the water and put on the iron boots, go down the passage, and remove the boots to float up.
Climb out of the water and shoot the Tektite that is across the gap. Then hit the switch on this side to make a spout of water come up. Carefully jump onto the spout, and jump to the other side from there. If you fall below, you must hookshot the starting ledge and try again. After you have gone across, go through the door.
The water in this room is swirling counterclockwise. There is an underwater ledge in the corner opposite from the one where you entered the room. Get in the water and let it take you to that corner, then put on the Iron Boots and try to land on the underwater ledge. When you are standing on it, position yourself so you can see the Hookshot target on the wall in the tunnel, then use the Hookshot to hit the switch in the dragon's mouth, then use the Hookshot on the target on the wall. Go through the gate, avoid or kill the Shell Blades (but try to go to the other side of the gate before it closes), then take off the Iron Boots to float up to a chest that contains a small key.
Get a Gold Skulltula
Hit the crystal switch and get in the water and put the Iron Boots back on, then go past where the gate opened, go to the large part of the room with the swirling water, then take off the boots and leave the room through the door that you came in.
Kill the tektite, then use the Hookshot on the target across the gap. Get in the water at the end and put on the Iron Boots. Go to the end of the hallway, then use the Hookshot on the target up above to reach the ledge.
Before moving on, there is a gold skulltula you can get now. First, look for the locked door in the base of the tower. There is a passage in the wall across from it. Go through that passage. You will find a cracked floor. Bomb it, then get into the water and put on the Iron Boots. Kill the Shell Blade that is in the way, then go to the end of the passage and remove the Iron Boots. Get on the ledge and step on the switch to raise the water a little bit (only in this room). Use the Hookshot on the dragon, then kill the tektites on this ledge. In the 3DS version, hit the crystal behind the dragon to open the gate. In the N64 version, spin attack the gate (or just slash it with Biggoron's sword) to open it. Kill the gold skulltula to get the token. Return to the central room.
Raise the Water
Go through the locked door in the base of the tower.
Walk to the end of the short walkway and turn around to see a hookshot target up above. Use it and you will reach a ledge with another Triforce symbol. Play Zelda's Lullaby, and the water level will rise a bit, but not all the way.
Get a Third Key
The water has caused a block to float up. There is a hole under that block that you need to go into, but there are spikes on the floor to either side of the walkway down below, so you need to be careful. Get in the water and position yourself between the floating block and the ledge with a door on it. Put on the Iron Boots, then fall into the hole under the floating block.
In the room ahead, there is a crystal switch. Stay near the entrance and hit it with the Hookshot. Shell Blades and Spikes will fall from a gate in the ceiling. Carefully kill them all to cause a different ceiling gate to open. Stand under the gate that just opened, remove the Iron Boots, then open the chest up above to get another small key.
Get a Fourth Key
Return to the tower room by floating up through the hole that you came down. When you are above water, stand on the ledge. You may notice a Gold Skulltula up above. However, you can't get it yet, so you will have to come back later. Exit the tower.
Outside the tower, get into the water and put the Iron Boots on. Go to the passage that has two unlit torches next to it, and go into the room where you met Princess Ruto earlier. Remove the Iron Boots and float up. Now that the water level has changed, you will reach a new area that was not accessible before. Bomb the cracked wall. Go through and open the chest to get another small key.
Get the Compass
Get in the water and put on the Iron Boots, then go back to the central room with the tower. Take off the boots and turn around to see a passage with two pots on it. Go into that passage. When you reach the spikes at the end, use the Hookshot on the target up above, then turn around and use the Hookshot on the target on the ceiling. There is a big chest in this room that is blocked by a water spout. The crystal switch in the corner lowers the water, but the water only stays down for a very short time, so you should stand near the chest (or in the N64 version, you can float to the top of the water spout) and shoot the crystal switch with an arrow. Then quickly open the big chest to get the Compass.
Raise the Water Again
Use the hookshot on the target down below so you can avoid landing on the spikes. Jump over the spikes and return to the center room. Go around to the other side of the room where there is a locked door in the wall. Unlock it to go to the next room.
You need to go through the hole in the ceiling, but in the N64 version, the Tektite up above will try to hit you on the way up, so if playing the N64 version, before you go up, stand on the water spout to lure the Tektite down and kill it.
Stand on the spout and use the Hookshot on the crystal switch to be sent up through the hole in the ceiling. Go through the door. You will find another Triforce Symbol. Play Zelda's Lullaby to raise the water to the highest level.
Reach the Mini Boss
Above the water, there is a locked door in the west wall (don't go through yet), the exit from the temple in the south wall, a dragon in the north wall with a Hookshot target that is too far for you to reach, and a passage in the east wall. Go through the east passage until you find a block in the wall (the path around the corner just leads to a dead end.) Pull the block until it stops.
Go back to the center room and go through the locked door in the west wall.
First, kill the keese with the hookshot. Then walk slowly straight ahead until you fall off of the ledge and onto a platform. Again, go forward slowly, and this time the platform that you land on is moving. Use the Hookshot on the target of a falling platform, then do it again until you have reached the top. Unlock the door to reach the next room.
Use your arrows to kill the three tektites in the water before proceeding. When they're all gone, use the Hookshot on the crystal switch in the center, or an arrow if you have trouble reaching it with the Hookshot. This will raise the water level (in this room only) and raise the dragon heads. Use the Hookshot on the dragon nearest you, but don't go any farther. Hit the crystal switch to lower the water again. Then use the Hookshot on the wall next to the second dragon's head, then climb over the head to face the crystal switch again. Hit it, use the Hookshot on the final dragon, hit the switch again, stand on the dragon's head, and hit the switch one last time to be sent upward to the door. Kill the tektites first, then kill the Like Like across the spikes with two arrows (the arrows can't go between the spikes, so shoot over them), then use the Hookshot on the ceiling beyond the spikes. Go through the door.
This strange room appears to be outside. There is a tree in the center and a locked door at the other side. Walk to the locked door, then start walking back slowly, and keep an eye on the tree in the center. After you walk between the doors of the room, you see a shadowy something by the tree. If you get close to it, you engage in a fight with Dark Link (or Dark Whatever-your-name-is).
At first, Dark Link might not attack. Do a backflip or side jump to make him start attacking.
If you want to battle Dark Link with just the Master Sword, it can be tricky, but not impossible, because he will jump on your sword if you stab it at him, and if you swing the sword, he will swing his at the same time, making the swords bounce off of each other. One way to hit him with the Master Sword is to wait for him to hit your shield with his sword, then do a jump attack afterward. You have to time it properly and be the correct distance away from Dark Link for this to work, but it's not too hard. Another way is to shield yourself from Dark Link's attacks without targeting him, then hit Dark Link while crouched.
After you hit him, he reappears behind you, so be careful. Don't try turning around right after hitting him, because he will just appear behind the new direction that you are facing. Instead, wait for him to reappear, and turn around as soon as he does.
If you have Biggoron's sword, this battle is as easy as stabbing it (not swinging it) at Dark Link a few times until he dies.
Alternatively, you can hit Dark Link with the Megaton Hammer and he can't defend against it.
Another option is to use Din's Fire, but you might run out of magic before Dark Link dies.
In the N64 version, if you throw a Deku Nut next to (but not directly at) him, Dark Link will be stunned, then will not attack anymore after he recovers.
Get the Longshot
After you conquer yourself, the room transforms back into a normal temple room, and the doors open. Go through the north door. Open the chest to get the Longshot. It replaces the Hookshot and works the same way, but extends twice as long as the old one.
Get a Second Gold Skulltula
Don't leave the room! Instead, go behind the treasure chest and play the Song of Time to open the hole in the floor. (It is harder to see this in the N64 version.) Go into the hole to find an underground cave and small river. There are vortices in the water that will drag you down and kill you if you get too close. You can't wear the Iron Boots near the vortices because you will just slide down into the vortex.
Go to the far right side of the ledge and get in the water there. Stay on the left side and swim past the first vortex on the left. After you get past the vortex, put on the Iron Boots, then walk up toward the Gold Skulltula on the wall up ahead, then use the longshot to kill it and get the token. Remember not to try walking past the vortex while wearing the Iron Boots: you will just slide down into the vortex.
Get a Fifth Key
Go to the far right side and remove the boots and swim past the next vortex. The third vortex is the hardest to stay out of. You can't walk past it with the Iron Boots or you will slide into it, so just stay very far to the right and swim as fast as you can (tap the sword button repeatedly to swim faster) to reach the little ledge just beyond the vortex, and climb up. There is a fairy in the jar on the left, but be careful not to fall into the water if you hit it.
Then look across the water and use the Longshot on the target above the ledge to land there. Use an arrow on the eye on the wall across from you, then quickly use the Longshot on the chest inside the gate to get in. Open the chest to get another small key.
Get a Sixth Key
Go through the passage beyond the chest. This is the room with the swirling water that you visited earlier. Use the longshot from here to reach the ledge with the door. Go through it.
Lower the Water Again
Use the Longshot to go across the gap, then get into the water up ahead and put on the Iron Boots. When you reach the end, just take off the Iron Boots, then swim into the passage. Put the Iron Boots back on and go to the room where you met Princess Ruto (the passage is in the east side of the ground floor. Take off the Iron Boots and float to the top, and play Zelda's Lullaby to make the water go to the lowest level.
Raise the Water Again, part 2
Fall down below (you won't get hurt), and go back to the big central room. Go into the tower and raise the water with Zelda's Lullaby. (Note that there was no way into the tower when the water was at the highest level, so that is why you had to lower it all the way first.)
Get a Third Gold Skulltula
Before you leave the tower, use the Longshot to kill the Gold Skulltula up above and get the token.
Get a Seventh Key
Leave the tower and go around to the other side. Look at the wall and you will see an eye switch under the water. Shoot the eye with an arrow, then quickly use the Longshot on the target beyond the gate. Go down the passageway and push the block as far as it will go (you pulled this same block earlier) and go to the right to get another small key.
Get a Fourth Gold Skulltula
The path to the main room is blocked now. Leave the room where you got the small key and go straight ahead to find a hole in the ceiling. Use the Longshot to go up, then go through the passage. You will be back in the central room.
Get in the water and use the Iron Boots. Go into the passageway in the north wall. You will fall down a short distance. Go to the end of the path, then remove the Iron Boots. Get up on the ledge, then use the Longshot to go over the spikes. Go through the locked door.
If you can, kill all of the tektites before continuing. You can stun the four nearest Tektites with the Longshot to make them jump toward you so you can kill them with your sword (if they stop approaching, stun them again). You will need to use arrows to kill the two farthest Tektites.
There are vortices in the water, and boulders will roll through the water as well. Make your way across the room, staying away from the vortices and avoiding the boulders as you swim. After you go across, go through the door.
Don't go down below yet. Stand at the edge of the ledge, and shoot arrows at the Stingers below. Some might fly up to you, so be prepared to swing your sword at them. After you kill all of the Stingers, go down below and climb onto the wide ledge. If there are any other stingers, kill them before proceeding. Bomb the wall at the end of the ledge. Go into the passage, then push the block as far as it will go. Then go back to the water, swim across, and bomb the wall on the short ledge that doesn't have jars on it. Go into the passage and pull the block as far as you can. Then go through the other side of the passage and push the block off of the ledge. The water will rise (in this room only). Go up the stairs and exit this room.
Shoot the Tektites across the gap if you wish. The floor switch will make three water spouts rise. Step on the switch and carefully jump across to the door. Exit.
Go to the end of the passage, but don't walk forward into the water. First, put on the Iron Boots, then wait for a boulder to pass, go down into the water. Turn right, and quickly use the Longshot on the Gold Skulltula to get the token.
Get the Boss Key
Now go as far forward as you can (in the same direction where the Gold Skulltula was) until you sink below. Kill the Shell Blade and go to the end of the pasasge, then take off the Iron Boots and climb up. Go through the locked door, then open the chest to get the Boss Key. There are two fairies in jars here, so catch them in bottles if you wish. Exit.
Get a Fifth Gold Skulltula
Get into the water, but be careful of the Shell Blade down below. Put on the Iron Boots and kill the Shell Blade, then go to the end of the passage. Take off the Iron Boots. The water will push you into the room with the Tektites, vortices, and rolling boulders. In this room, go to the door on the right (near the ledge that you came from), and go through the door. Use the Longshot on the target across the gap, get in the water and put on the Iron Boots, then walk to the center room.
Take off the Iron Boots to reach the water's surface. Go through the door in the west wall. Go up the water spout again, then go through the door at the top and play Zelda's Lullaby to raise the water once more. Before continuing, go through the door in the west wall to reach the room with the falling platforms. Use the Longshot on the Gold Skulltula on the right wall.
Go to the Dungeon Boss
Finally, go back to the tower and go to the north side. You will see the big dragon head to the north. Use the Longshot on it to go across. The jars here have fairies inside. Go through the door.
You need to run up the slope past the Razor Traps, but it's slippery. If you go at too much of an angle as you run up, you will slip down, so you need to watch the timing of the Razor Traps and wait until it will be safe to go up in a mostly straight line. After you reach the top, go through the big door.
Jump onto one of the four platforms in the pool. There will be a cut scene.
When the battle begins, jump off of the platform and climb onto the ledge around the pool. Morpha will shoot tentacles of water at you, and they will grab you if you are too close. You can completely avoid them by staying in a corner of the room. From there, keep trying to use the Longshot on Morpha's core. If you hit it, you will pull it toward you out of the water. If you can, try to trap the core in a corner. Hit it with your sword. If it goes back into the water, you will need to pull it out of a water tentacle again. A second tentacle will come out of the water as well, but you will be safe if you stay in a corner. Repeat the process until Morpha dies.
Get the Heart Container from next to the warp spot in the pool, then warp out of the temple.
After the cut scene in Lake Hylia, quickly run to the little stone platform on the east end of the island that you are standing on. The sun should be rising now, so shoot at the sun with an arrow. If you did it correctly, a special arrow will fall from the sky. If the sun goes too high before you shoot the arrow, just change it from day to night to day, and shoot the sun when it is near the horizon. When the special arrow appears, swim out to the little platform where it landed, and collect it to get the fire arrows.
Swim back to the island from which you shot the arrow. Use the Longshot on the top of the tree so that you land on the high branch. Turn it to night, and a Gold Skulltula appears on the tree. Use the Longshot on it to get the token, then go back down to the ground.
If you haven't already, go into the Lakeside Laboratory and jump into the water. Put on the iron boots and sink to the bottom. Roll attack the crate to reveal a gold skulltula. Kill it with the Longshot and get the token.
Also, if you won the Golden Scale from the Lake Hylia fishing game, dive to the bottom of the water in Lakeside Laboratory, then talk to the Lake Scientist to get a Piece of Heart.
Also, if you planted a bean outside of the Lakeside Laboratory in the past, ride the bean sprout up to the roof and climb the ladder to get a Piece of Heart.
Go to Kakariko Village. There will be a cut scene. Afterward, Sheik teaches you the Nocturne of Shadow.
If you don't yet know the Song of Storms, go into the windwill and go up to the angry-looking guy and use your ocarina. He will teach you the Song of Storms (only if you are adult Link).
Go to the Past
Play the Prelude of Light to return to the Temple of Time, or if you have not learned the Prelude of Light, just save the game when you are outside, then quit the game and start again. You will start in the Temple of Time. Put the Master Sword back into the pedestal to return to the past.
Go to Kakariko. If you warp there with the Nocturne of Shadow, you can't get very far into the Shadow Temple as a kid, so just climb over the fence to reach the graveyard. From there, go into the town itself.
Enter the windmill. Mute the sound if you don't like it when music changes pitch. Play the Song of Storms inside the windmill and it starts spinning like crazy, and all the water in the well is drained. Climb down into the well and you will see a path. Go into it.