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As you enter, crawl through the hole right in front of you. Once done, climb down the ladder. Right on the way is a Redead, get behind it and kill it if you want, then progress to the main area.

Bombing the rubble to the left of the barred passageway leads to a small cave with some recovery hearts, which is helpful to know for later. For now, go to the left and into the first alcove. Bomb the rock here to uncover an eye switch, hit it with your slingshot and you'll see a grating open somewhere else. Now, go around the level following the water until you see two rocks to your right, lay a bomb to blow them up. Throw another bomb to kill the Skulltula hanging from the ceiling just behind. Run behind to find a switch, trigger it to open more gratings.

Now, go back to the passageway and follow it clockwise until you come across a large Triforce symbol on the ground. Play Zelda's Lullaby here to open the other gratings. Look carefully at the right hand of the statue and you should notice a crystal switch sticking out, hit it to drain the well. Now, turn around, go straight to the treasure chest and open it to get the Dungeon Map. Go to the left and you should find an open cell with a crystal switch inside, hit it to open the door on the other side. Do not enter the door for now, but return to the beginning area.

Now that the well is drained, you can jump down into the hole. Crawl through the crawling hole there, then climb up the vine and go through the door to get to the miniboss of this dungeon, Dead Hand. He works just like in regular OoT - get grabbed by one of the hands, then wait for him to come to you and slash him when he lowers his head. Once he's gone, a treasure chest will appear which contains the Compass. Do not leave yet, but bomb the top left rubble to obtain a small key. Now, return to the beginning area.

First Well Skulltula
After getting the Lens of Truth, take the northeast passage. It is full of invisible Skulltulas hanging from the ceiling, and at the end you'll find a Gold Skulltula.

Once back there, go to the northeast corner and crawl through the hole there. Once there, note that the door is locked, with seemingly no way to open it. But look carefully at the face on the wall to notice a tiny bit of a crystal switch sticking out - hit it to unlock the door, then go through it. The next room has a Floormaster and Wallmasters but simply go through and open the locked door at the end. There, bomb the rubble to reveal a switch, stepping on this switch makes another grating open. Now, return to where you found the Dungeon Map and drop down the now open hole behind it.

Step on the switch to make a treasure chest appear, then jump off the platform. Head to the southeast passageway, and once there play the Sun's Song to freeze all the Redeads hiding in the corner. Don't bother with them, instead run to the treasure chest and open it, it contains the Lens of Truth, which lets you see hidden enemies, passageways and fake walls. Now run back and climb the ladder all the way up to return to the main room.

Second Well Skulltula
Get to the door to the west of the Dungeon Map. Watch out, the room behind it is full of invisible monsters. Pull the grave there to reveal the Gold Skulltula.

Now, return to the door to the east of the Dungeon Map which you opened earlier. Inside, the room looks like a giant pit but by using the Lens of Truth, you'll be able to see the safe passage through. At the end, you'll find a small key, collect it and return to the beginning area. Unless you intend to collect the third Gold Skulltula in here, this key is useless since you're already done here, so leave the well the way you entered it.

Third Well Skulltula
Get to the west passageway. Drop down, climb the vines, and use the small key you collected to open the locked door. Watch out, just behind the door stands a Gibdo, so immediately pull out the Ocarina and play the Sun's Song to stun him. Go all the way to the back and you should see the Gold Skulltula hiding behind the right bird statue. Do not light the torches here, they will just reveal more Gibdos which you definitely don't want.
The Legend of Zelda: Ocarina of Time Master Quest
Return to the Ocarina of Time guide at Shadow Temple