NOTE: This Walkthrough will cover, each and every Heart Piece, Item, Boss, and everything else.
Since you let the water through in the Light World, it is still as is in the Dark World. Head up and jump into the water. Swim to the left and up the broken ladder.
Kill the three enemies here to make a chest appear. Open the chest for a small key. Go through the locked door and down the stairs.
Head down a little bit and then left. You will notice that the wall here can be bombed. Place a bomb to make a hole appear. Walk through and head left to find a chest. Open the chest for the dungeon map. Head back right a screen.
There are four jars in the center of the room. The one at the very bottom holds a small key. Grab it and then go through the locked door at the bottom-left of the screen.
Kill the enemies here and then head left. Go down the stairs and up into the next room. Lift the pot there to get another small key. Exit down.
Now head up the other set of stairs and go through the locked door. Kill the enemies here and then pound the moles and push the lever to the left to let water fill up the ground below you. If you want 5 rupees and a bomb, you can blow up the hole on the left side of the screen. Afterwards head back down. Jump into the now risen water and swim to the left. Head up the broken stairs and exit left.
You are now in the center room of the dungeon. The big chest is in the center of this room but cannot be opened just yet. Go through the door at the bottom of the room. Head right and follw the path down a room. Head left and follow the path up a room. Push the bottom block to the right to make a chest appear. Open it for the compass. Head up a screen.
Go directly left and head up the first stairs you can see. Head through the door at the bottom-left of this huge center screen. Head down the stairs and up through the door. Lift the pot and grab the key. Exit down. Head back up the stairs and right a screen. Now head to the stairs located at the top-left of the main room. Go through the locked door.
Kill the two enemies here and then hit the orb so it is on red. Push the lever to the left so water will flow below you. Hit the orb back to red and exit the room to the right. Back in the main room again, go through the door at the bottom-left once again. Head left and jump into the water. Swim to the left and go through the door.
Kill the enemies here and then go down the stairs on the left side. Push the bottom block to the left and the middle block up. Head up the stairs and head up the stairs at the top of the screen. This next room could be a pain becaose of all the enemies. You could use the Cane of Bryna for some extra protection if needed.
Head to the top-left and push the block up. Fall down the hole and open the chest for 20 rupees. Jump off the platform here. Head down and left. Move the blocks the same away. Head up the stairs and up the other stairs once again. Back in this room again, but this time head to the top-right. Push the block up and fall down the hole here.
Lift the pots for some rupees. If you followed the walkthrough the orange blocks should be down allowing Link to get to the room to the right. Do so and lift all the pots for some rupees. Then open the chest for the Big Key. Head back left a room and jump down. Head down, up the stairs, and right a screen. Jump in the water swim right and out of the water. Head right a screen so that you are back in the main room.
Now that you have the Big Key, head to the center of the main room and open up the big chest to get the Hookshot.
From the platform that the Big Chest is on. Go to the center of it and look to the right. You will see a jar. Use your hookshot to hook onto it. Once you are on that platform, lift the jar on the right side to get a small key. Jump back down and then get back onto the platform with treasure chest. Go directly above the chest and look up. There are some more jars there. Hook onto them and go through the locked door at the top.
Once you are in this room, head to the left and kill the enemy. Lift the upper-left pot and push the statue onto the switch to keep the door open. Dont go through the door above you, but instead go to the right side of the room and go through the now open door on the left side.
Head up killing the enemy. Go down the stairs. Push the lever. Go down the stairs and head left a screen.
Go down and through the door on the right. Lift the pots and open the chest for some rupees and some hearts. Head back left a screen. Go all the way up through the door at the top. Head up through the door here and lift the pots here for some items. Head back down a screen.
Go to the third block from the left and push it to the right. A Treasure chest will come up. Open it for 20 rupees.
GO all the way to the right of the screen. The second waterfall from the right is the way to go. Just walk up through it to get to the room above. Kill the enemies and lift the pots for some items. Head up the stairs. Kill the enemies and head down a screen.
Jump in the water and swim to the right. Go up the stairs there and lift the jar for a key. Jump back into the water and go to the next ladder to the left. Place a bomb against the wall at the top and go through. Lift all the jars for some items and then head back down. Jump back into the water and swim to the last ladder on the left. Go through the locked door. Head up and enter the Boss Room.
A fun battle with Arrghus here. TO defeat his first stage, hookshot the small cloud looking things around him and hit them with your sword repeatedly. Keep hookshooting and hitting them until all of them are gone. Watch out because he will release all of them in a big circle as an attack. Try to stay as far away from him.
After all his little friends are defeated he will go off screen and fall into the water. He will move quickly in the water trying to attack Link. Simply strike him with your sword and he will go off screen once again and fall down again. Repeat this until he is gone.
Grab the Full Heart Container after you defeat him.
Also grab the crystal and listen to the maiden. The maiden will tell you you about Ganondorf, the Triforce, and some hints throughout the land. Afterwards you will be teleported to just outside the dungeon.