Along your adventure you should have picked up the Song of Storms by completing this quest, and if you haven't then do it now. You need the Song of Storms to continue.
Go to Kakariko Village and head up to the wind mill. Inside you will find the same guy who taught you the Song of Storms in the future. Play that song for him now.The wind mill will begin spinning out of control, sucking all the water out of the well. Don't ask me how that works. Make your way into the well now that it's open.
When you enter, start by going through the hole in the front wall. Jump down the ladder and fight the Skulltula in this hallway. At the end of the hallway Navi will zoom to a skeleton, tell you that they are talking and tell you that it is saying to "Look for the eye of the truth...". That's what this dungeon is for, to find the Lens of Truth, which you need to proceed.
As you may now have guessed, everything you see is not exactly true. Example: Walk through this wall in front of you. Enough said?
You've now entered the main room of this dungeon, which I will now refer to as the main chamber. There are tons of false walls around here and, if you accidently fall into one, ignore it! Following it could get you into a sticky situation. This walkthrough will lead you back to it, so don't worry about it until its needed.
Start by going to the far side of the main chambers and look for a hallway being guarded by a Skulltula. Walk to the end of it and you will fall through the floor. Bomb the boulders in this hallway to continue. It's a good idea to take out the enemy who screams at you here. All you have to do is make sure to stay behind him and then nail him with your sword a bunch of times. Down one of the other corridors you will find the Dungeon Map. Collect all the silver coins in this room to open the door. Two are in the pool in the middle of the room and the other two are up the ladder, this ladder leads to the door out.
One of the walls in this room are fake, go through it to find yourself back in the main chamber. Halfway down the west wall, or, to the left twice from where you are now, you will find a hallway that has a pool in it, and a fence across it. Dive under the fence and go through the door on the other side. Use a deku stick to light up all the other torches in this room and find the grave that has the key in it. Once you've found it exit the room and go back out into the main chambers.
At the very back of the main chamber you will find a tri-force on the ground that you can play Zelda's Lullaby on. Doing so will change the water, and doing this the first time, moves the water level down.
Now go back to the entrance of the dungeon and you'll notice a hole in the ground that used to be full of water. Drop down into it and find the hole and crawl though. Kill the Skutlltula and go through the door at the ned of this room.
This is a mini boss room where you must fight Dead Hand. Let one of the hands grab you to get a start. After Dead Hand surfaces you can attack his face when he bends it over. Hit him ten times to proceed. Your reward is the Lens of Truth!
Go back out to the main chambers and look towards the center of the room using the Lens of Truth. Now you should be in the center of the main chamber. Navi will warn you about creatures on the ceiling, so let it fall and then attack it with your sword so it won't pester you while your busy reading this guide. Now exit the center of the main chambers and circle the path that the green skull thing takes and take a look for other things in the center pillar that couldn't be seen. Doing so will reveal two crevaces that hold keys in them. Once you've found them go back to the center and keep the Lens of Truth on. Be sure not to fall down any of the holes. In here you will find two rooms that need keys.
Once of them has a Gold Skulltula in it. The other, however, has what appears to be only a hole in the middle of the room that you can't cross. Use the Lens of Truth to reveal a small walkway around the outter ledge of the room that you can use to get around the hole.
In the center of the main chambers you will see a cell with a chest in it. You won't be able to get at it from here, because there will be a hole in the way of the entrance. Look inside the room and you will see an entrance from the back, go around and use it to open the chest and receive the Compass.
Now go to the north east portion of the main chambers and you will find an entrance with a hole in it. Crawl through it to the other side. Use your key to gain entrance to the room. Inside you will find a bunch of bats and a Beamos. Use your Lens of Truth to make your way across the room, as there are many holes you have to dodge.
In this small cell you will find one last Gold Skulltula. You are now done with the Bottom of the Well; time to make your way to Kakariko's Graveyard.
