Go to Lake Hylia. There's only a little bit of water in the lake now. Get in that small bit of water and put on the iron boots, and use the hookshot on the diamond-shaped thing to open the gate. Go in.
This is one of the hardest temples you have to beat in this game. 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. If you follow this guide you'll have no problem.
NOTE: As I said, there's a hard mini-boss in here that's much easier to kill if you have Biggoron's sword (instructions on how to get it are in "Getting Biggoron's Sword"). You can also use Din's Fire but may run out of magic, so you can also opt to bring in some green potion. Deku Nuts also work.
Enter the Temple
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 spiky monsters bother you, use your shield or hookshot to make their spikes retract, then hookshot them again to kill them.
One of the paths down here has two unlit torches to either side. Go through that one and around the corner is none other than a grown-up Princess Ruto. Listen to what she has to say (including yelling at you... just like old times, huh?) then watch her float up. Stand under her shadow and take off the iron boots to follow her.
Up above she's nowhere to be found.... Go through the door here and kill all the spiky guys to make a chest appear containing the map.
Get out of that room and go over to the wall with the Triforce symbol on it. If you check on it, it says something about the royal family of Hyrule, indicating you should play Zelda's Lullaby. If you use your Ocarina in the right spot, a musical staff will appear. When it does, play Zelda's Lullaby, and the water in the palace drains completely. You have to hop down the hole you floated to when there was still water there. It's a long way down but this is a special case where you don't get hurt when you land. Just jump.
Down here are two unlit torches and a lit one in the middle of the room. Shoot an arrow through the flame of the lit torch at each unlit torch in turn. (You could use Din's Fire, also, but it uses a lot of magic.) The door is unbarred; go through.
There are three shell blades here. You have to hookshot the soft innards inside the shell when it's open and facing you to kill it. If you don't do it in time, the shell will close, turn around, and try to impale you with the spikes on its rear-end. Kill the Shell Blades to make a chest appear containing a small key.
Exit and return to the big main room which is now drained. Kill the tektites and spikes. Across the way from where you come out (around the central tower) a giant block is in the wall. Get up on the platform 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.
Across the way, a tektite is just sitting there. You have to get over to that side, so use your arrows on it. If you can, kill it. If not, it will jump into the gap below, where it can't hurt you. Hit the switch on this side to make a spout of water come up. Carefully jump onto the spout, and from the spout jump across to the other side. If you fall below (where the tektite might be) you must hookshot the starting ledge and try again. Once across, go through the door.
The water in this room is swirling counterclockwise. There is a ledge in the opposite corner under the water, so jump in, wait until you're at the opposite corner, put on the iron boots, and try to land on the ledge. Once you're standing on it, you can hookshot the switch in the mouth of the dragon, then hookshot the target on the wall and run into the gate. Avoid the shell blades (don't waste time killing them) and take off the iron boots to float up above to a chest containing a small key. Hit the crystal switch and sink back down with the iron boots, avoiding the shell blades as best you can, get into the swirling water, take the iron boots off and pull up onto the ledge with the door going back the way you came.
Killing the tektite, hookshot the target across the way and go through the door, and make your way to the central room with the big tower. To get up from below you need to hookshot the target above; the water is too low to reach the ledge.
Before moving on, there's a gold skulltula you can get now. First, go through the passage across from the locked door in the tower. Bomb the cracked floor and sink down below, kill the shell blade, float up and step on the switch to raise the water a little bit. Hookshot the dragon, kill the tektites and spin attack the gate (or just slash it with Biggoron's sword) to open it, and kill the gold skulltula for the token. Return to the main room.
Find the locked door of the tower and go through.
Walk to the end of the little walkway and turn around to see a hookshot target up above. Use it and you reach another Triforce symbol. Play Zelda's Lullaby, and the water level rises a bit (not all the way). Notice that a block that was down below has floated up. There's a hole where it was that you want to fall into, but be careful; there are spikes to the left and right of the walkway below. Center yourself between the two platforms before putting on the iron boots. Walk to the newly revealed hole to fall in.
In the room ahead is a crystal switch. Stay near the entrance and hit it with the hookshot to cause some spikes and shell blades to fall from a gate in the ceiling. Carefully kill them all to cause a different ceiling gate to open. The gate the monsters fell out of is empty, so float up through the other one for another small key.
Return to the tower room by floating up through that hole. Just keep floating up, and pull up onto the ledge. Exit. Get into the water that is now here and put the iron boots on. Go into the same room where you met Princess Ruto and float up, where you access a previously unreachable area that you can now get to now that the water is at the new level. There's a cracked wall here; bomb it to get another small key.
Use the iron boots to get back down and out to the main central area. Take off the boots and turn around to see a passage with two pots on it. Get rid of the tektites and get into that passage. Follow the path and you see a hookshot target up above, so hookshot it, then turn around and hookshot the ceiling. You're in a small area with a big chest inside a spout of water. The crystal switch lowers the water but only VERY briefly. Your best bet is to get around the side of the chest you can open, and get into the spout of water so you're floating on it. Stand in such a way that when the spout goes down, you're standing in front of the chest and can open it quickly. Once you're ready, hookshot the crystal switch and quickly open the chest for the compass.
Go around to the far edge of the hole so that when you jump down, you don't land on the spikes. Return to the central area. Swim across to the opposite side (around the tower) and get up on the block and unlock the door to the next room.
Get near the spout to lure a tektite down from above so you can kill it and get it out of the way. Then stand on the spout and hookshot the crystal switch to be sent up through the hole in the ceiling. Go through the door. There's another Triforce symbol here, so play Zelda's Lullaby yet again.
Opposite from the locked door (don't go through) is a path with a block you can pull, so do it until it stops. Return to the main area and go through the locked door across the way.
First, kill the keese with the hookshot. Then walk slowly straight ahead until you fall off the ledge and onto a platform. Again, go forward slowly, and this time the platform you land on is moving. Your goal is to latch onto one of the falling platforms in front of you with the hookshot from here, then continue grabbing the falling platforms until you reach the top. The platform you're standing on has to be pretty far down for your hookshot to be able to reach one of the falling platforms. Once you can reach, latch on and start hookshotting your way up. At the top, hookshot the ledge to get to the locked door leading out, and go through.
Use your arrows to kill the three tektites in here before proceeding. When they're all gone, hookshot the crystal switch in the center (if it's ever too far just use an arrow, but it should never be too far) to raise the water level and raise the dragon heads. Hookshot the dragon nearest you, but don't hookshot any further. Hit the crystal switch to lower the water. Hookshot the wall next to the second dragon's head, then climb over the head to face the crystal switch again. Hit it, hookshot the last 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, then hookshot the ceiling. Go through the door.
This strange room appears to be outside. There are actually invisible walls around so you can't walk too far. There's a tree in the center and a locked door at the other side. Walk towards the locked door then start walking back slowly. If you stop before reaching the tree and take a close look you see a shadowy *something* by the tree. Get any closer and you engage in a fight with a creepy shadow of Link, a.k.a. Dark Link (or Dark Whatever-your-name-is).
If you have Biggoron's sword this battle is as easy as thrusting it at Dark Link a few times until he dies. It has to be a straight thrust and not a swing. If you're stuck with the Master Sword, things will be much more difficult. If you're using the Master Sword, your real sword will bounce right off his shadow one (since he mirrors your moves) and no damage will be done. But Biggoron's sword doesn't move the same as his Master Sword and will thus get through his defense. The spin attack with the Master Sword may actually work, so give that a shot and see if you can get some hits in that way. Otherwise, aside from plain blade attacks, most any attack you can think of, he'll sidestep or otherwise avoid. You can use Din's Fire, but you will probably run out of magic before you can kill him with it. Deku nuts also work, but you have to use a ton and may run out of those too. Using a combination of Din and deku nuts may do the trick. There ARE ways to hit him without a spin attack but they're very tricky. Try to swing your sword after he does, or move around a lot as you swing, and if you get sick of it or are dying break out Din's Fire or some deku nuts. Good luck.
Now that the shadowy figure is finally gone, the room transforms back to a normal temple room, and the bars on the far door open, so go through. Inside is a chest with this dungeon's prize: the Longshot. This replaces the hookshot and is basically the same item, but it extends twice as long as the old one.
DON'T leave this room yet, there's actually a block in the floor behind the chest that can be removed with the Song of Time, so walk to it and play the song and it disappears. Drop through. You're in an underground cave with a little creek, and there are some vortexes here that will suck you in and kill you if you get too close. Get off the ledge at the far right, stay to the left side of the creek and swim past the first vortex to the left. Put the iron boots on after that and walk up towards the gold skulltula, then use the longshot to kill it and get the token. Get to the far right and remove the boots and swim past. The third vortex is the hardest to stay out of, stay very far to the right and swim as fast as you can to the little ledge just beyond it, and climb up. Then longshot the target above the ledge across the way 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 for another small key.
Down below is the room with the swirling water. You can use your longshot from here to get to the ledge with the door out. Exit.
Go to the main area and put on the iron boots. Sink to the bottom and go to the room where you met Princess Ruto, float to the top, and play Zelda's Lullaby to make the water go away. Drop down below, go into the tower and raise the water with Zelda's Lullaby. While here, longshot the gold skulltula up above for the token. Leave the tower and walk around to the opposite side for an eye switch in a little niche in the wall below a gate. Hit the eye with an arrow then quickly longshot the target beyond the gate to get in. Push the block the rest of the way here (you pushed this one earlier in the dungeon) to get another small key.
The path to the main room is blocked, so find the hole in the ceiling and longshot up. Go back out to the main area yet again. Sink to the bottom, and go through the passageway that has an arch. Float up, use the longshot to get past the spikes, and go through the locked door.
If you can, kill all the tektites with arrows before continuing. You can also stun the first two pairs with the longshot to make them jump toward you so you can kill them with your sword. The two far ones won't come within range. Make your way across the room staying away from the vortexes and avoiding getting hit by any boulders as you swim. Once across, go through the door.
Don't drop down just yet; stand above at the very edge and use arrows to kill the stingers below. Some may fly up to you; kill them with your sword. When they are gone, drop down and swim to the left-hand ledge. If there are any other stingers, get rid of them before proceeding. The ledge on the left side from where you entered has a bombable wall, so bomb it, then push the block as far left as it will go. Swim to the other ledge and bomb this wall, go into the passage and pull the block as far as you can. THEN go around the other side of the block and push it that one last step. Go back to the other side and pull the block as far as it will go, then get around to the other side of it and push it off the ledge to make the water rise. Go up the stairs and exit this room.
Use your arrows to kill the tektites across the way. The floor switch makes not one but three water spouts rise (and not in a straight line), so step on the switch and carefully jump across them to the door. Exit.
Go to the end of the passage and put on the iron boots. Wait for a boulder to pass then go into the passage, turn right and quickly longshot the gold skulltula for the token. Go as far forward as you can until you sink below. Kill the shell blade and go through the locked door and grab the boss key. There are two fairies in jars here, so catch them in bottles if you wish. Exit.
Float up and run straight ahead into the tektite vortex room. Swim to the door to the right and exit. Longshot the target, sink below, and get out to the main room.
Go through the door on this second level and follow the path, go out and play Zelda's Lullaby to raise the water once more. Before continuing, go through the door on this third level, into the room with the falling hookshot platforms, and longshot the gold skulltula on the right wall. Finally, go back to the tower and go around it until you see the big dragon head. Longshot it and you're across. There are more fairies in jars here, so get them if you need them. Go through the door.
You need to run up the slope here past the razor traps. You can't go too far left or right or you'll slip down and fall. You can't roll up the slope; all you can do is run up and try to avoid the traps. Time it so the first trap has just passed when you start running, and hopefully the others will move out of your way as you go up. Keep trying and eventually you get to the top. Go through the big door.
Jump onto one of the four platforms in the pool to start a scene. Morpha will come floating up out of the water. Jump off the platform back to the surrounding ledge. Morpha will shoot tentacles of water at you which will grab you if you're too close. You can completely avoid them by staying in a corner of the room. From there, keep trying to longshot the round body of Morpha from within the tentacle to draw it to you. Hit it with your sword and it will go back into the water. A second tentacle will come out at this point, but in the corner you're safe. Repeat the process until Morpha is gone.
Quickly run to the little stone platform on the far side of this island you're standing on, the sun should be rising so shoot at the sun with an arrow. If you do it right a special arrow will fall from the sky. If the sun goes too high or something just change it from day to night to day for the sun to rise again and shoot the sun. When you get it right, swim out to the little platform where the arrow fell and grab it to get the fire arrows.
Swim back to the island from which you shot the arrow. Longshot the very top of the tree here so that you land on the high branch. Turn it to night and a gold skulltula appears; longshot it and grab the token. Jump down out of the tree.
If you didn't before, walk to the lakeside laboratory and jump in the water. Put on the iron boots and sink to the bottom. Roll attack the crate down here to reveal a gold skulltula, kill it with the longshot and get the token. That's the last skulltula at Lake Hylia.
Also, if you didn't before, ride the bean sprout up or play scarecrow's song to get on the roof of the lakeside laboratory, climb up the ladder for a piece of heart.
Now it's time for a return to the past. Play the Prelude of Light (if you don't know it you can just save and reset to end up in the Temple of Time and learn the song from Sheik) and once in the Temple of Time, return the Master Sword to its pedestal to return to the past.
Go to Kakariko.
Enter the windmill. When you do what you're about to do next, the music speeds up and I think it's kind of creepy so I always mute it. 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 there's a path you can take.