Without a doubt this is the hardest temple in the game, and I’m sure a lot of people are jumping into this guide right here. If that’s the case, then you are probably stuck at some point in the middle of this dungeon. This dungeon is very complicated, so I suggest if your stuck that you run through and do everything on this guide, even if you already did it, so you’ll make sure to get anything you may have missed.
From the start: A little explanation. The hookshot and iron boots are key in this map. Watch as you enter this dungeon. You will, just as your entering, on the far wall, see a white and grey target. That is a hookshot target. Now you know. As for the map, it works on levels. You have the ability to change the water levels, which will change which doors you have access to. Basically the first time anyone does this dungeon it is just random luck and random floors until you find a room you’ve missed. Let’s get started.
Start by sinking to the bottom level by putting on your iron boots. Then head through the door to the east. It has two torches out front that are quite obviously unlit. In here you will meet Princess Ruto. Float up with the Princess to the next level. Don’t go through the door in this room. In this room, you will notice a triforce on the wall. That is the switch. Play Zelda’s Lullaby to make the water level change. This is the first of the three switches.
Go through the only open door in this room first and kill the three rocks inside. Hit them with your sword once to lower their armor and then whack them again to finish them. This gives you the Dungeon Map. Now go back out and change the water level. Once it’s finished fall to the bottom room.
Your now back on the bottom floor, in a room with one lit torch and two unlit. Use your arrows to launch an arrow through the flame and onto the other torches to get them lit. Be quick about it. Then go through the door.
The hookshot is your main tool in this dungeon, and you must now use it to kill these enemies. Just hit them when you see the pink side. You get the reward of your first key for completing.
Now go back out into the main chambers and go around to the other side. You’ll find a block you can push in. Follow the path it leaves through to the room with the huge hole in the middle and the crystal. Hit the crystal and wait for the water to spurt up. Then use it as a platform to jump to the other side.
In this room jump in the whirlpool and use your iron boots to make Link land on the pipe/platform to the north, not the dragon head one. You will see a little entrance way to the west with a hookshot target in it. You need to hookshot the crystal in the dragon’s mouth to unlock the door in the entrance and then quickly hookshot over and run through it. Here you will find yet another key. Exit back out to the main chambers.
Now look toward the center column. There is one locked door you can use to get in. In here you will find a few platforms with hookshot targets on them and a water level changer. Change the water level now. The video will show a block raising. Underneath it is a hidden passage. Use your iron boots to sink into it.
Down here will be a crystal. Hit it to make a stack of enemies come out. Defeat them, and in there you will find another passageway you can float up. Up there you will find a Key. Now go back to where the water level changer was. Go out the doorway there. Your now back in the main chambers.
Sink back down to the bottom level and go back through the doors that led to where you met Princess Ruto. Then float up to the second level, where you should find a wall that you can bomb. You get another Key. Now go back out to the main level.
On the second floor look for a platform on the second floor with two jars on it. It’s to the east. In there, after you walk through the passageway, you’ll have to go up two hookshot targets, where you’ll then find a crystal and a chest being blocked by water. Stand near the chest and then use your hookshot on the crystal, and quickly open the chest before the water turns back on. You now have the Compass. Then head back out to the main chambers and look for a door that you can unlock with a key. Ignore the one with the eye in front.
In this room stand on the water spout and then shoot the crystal with your hookshot to have it push you to the top and then head through the door.
Your now back at the top of the main chambers, and you can raise the water level back to the top.Raise it and then head to the east entrance on the top level and go in and find a block that you can pull out. Pull it all the way out and then go back out to the main chambers.
Now find the locked door on the top floor and go through it. This room can be a little overwhelming at first. I suggest starting by killing all of the bats on the walls. Then jump down to the bottom platform close to you, and then down one more. You have to use your hookshot on the other platforms and use them to slowly hookshot to the top.
Once you get through the locked door at the end of the room (you should have no more keys after unlocking it) you should end up in a room with a bunch of dragon heads and a crystal in the middle. If you do this right it may only take you one try, First, hit the crystal to raise the heads. Then hookshot over to the first platform. From there move the crystal down and then hookshot over to the second ledge. The dragon’s head is down, but there is still a hookshot target you can use. When you get to the second ledge jump over the dragon head and hit the crystal again to raise the heads. Then hookshot to the third platform. From the third platform lower the heads once more and use the dragons head to climb up to the door that leads to the next room. Just jump on it and hit the crystal again.
You’re now in a huge room that’s the surface of a pond with a dead tree in the middle. Now you get to fight the Mirror Link mini boss. Run all the way across to the other door, even though it’s not open, then turn around and wham! There he is! Some tactics:
The Biggoron’s Sword can make this a whole lot easier. Just keep whacking. He’s not half as good at blocking the Biggoron’s Sword as he is at simply mirroring the Master Sword. Also, you can use Din’s Fire. He gets hurt every time you use it.
After you defeat him head through the opened door on the other side. Your reward for beating Mirror Link is the Longshot. Twice as far a reach as the hookshot! Behind the chest in this room is a block of time. Play the Song of Time to have it removed.
Now you’re in a river. Just swim down it and make sure not to fall though the holes! Don’t worry, you have as many tries as needed. At the end you can longshot using the chest. Another free Key inside too.
Head through the door and you’ll find yourself back in the room with the dragon head. Make your way back out to the main chambers.
Sink the water back down to the bottom floor. Remember how to do that? Where you met Princess Ruto. Then go into the center column and raise it to the second floor.
On the second floor look for the door with the eye underneath it. Nail the eye with an arrow and then use your longshot to make it into the room on time by using the target at the end of the corridor. At the end of this corridor you’ll find the block you previously pulled out. Now push it in and a new passageway will be opened up. Go back out to the main chamber.
Sink to the bottom floor and go north. After you walk into the room, turn around and look up for a longshot target that used to be to far away. Longshot to it. Then longshot to the locked door.
In this room you should swim all the way to the back, whilst dodging the enemies, rocks and currents. A little hard but doable. Then go through the door at the end. Now jump off the ledge, kill all the little rays and blow up the walls that are cracked. Then push the block into the hole on the east side. Once you get the block in the hole and on the switch the water will rise giving you access to the other door in this room. In this room just step on the switch and jump across the platforms to make it to the other side. Then head through the door.
Now you’re in the stream. Head towards where the rocks are coming from, towards the waterfall and then use your iron boots to sink. Then go through the locked door to find the Boss Key.
Go all the way back to the main chambers, top floor, and look for the snakes head that used to be too far to reach with the hookshot. Longshot to it and go through the door.There are fairies in the jars.
Make it up the passage. It takes some precision and guessing. Just run up the sides and if you think your going to get hit and fall.
Jump onto one of the middle platforms to get started.
The nucleus is what you’re trying to attack. It’s the actual Morpha. The rest is just morphed water. When he comes up to grab you, hit him and pull him to you with your longshot (Z or L target) and then hit him with your sword.
Once you get outside the Water Temple it's time to go back to the past.