When you enter the well, there is nothing but a small hole in front of you. Crawling through will lead to a ladder. Climb or jump down to get your first view at this dark, trecherous place. Down here a redead waits. Playing the Sun’s Song can give you the advantage, though you should know how to deal with them by now. Eliminate him, and turn your attention to the skeleton on the wall. Navi will inform you that she can hear the spirits, and they’re telling you to find the “eye of truth”.
Head through the doorway. Immediately to your right there will be a pile of debris identifiable by the red crack running down. These piles can be bombed, sometimes discovering secrets underneath. Those without the red cracks will not be destroyed, so don’t waste your bombs if you’re looking for secrets. This one holds nothing, but the one straight ahead near some banded timber hides a chamber with some hearts in case you need health.
Follow the water around to the left, and the second entrance to your right will have some boulders in the way. Break your way in, deal with the Skulltula, and press the button switch. Walk back out (don’t bother with the hole, you can’t jump over it). Follow the water around the same way until you come to a large triforce painted on the ground. Play Zelda’s Lullaby to open the gate to the center room, and shoot the crystal switch the statue is holding to stop the water flow.
Head into the center room and claim your Dungeon Map. Navi may warn you to watch for shadows, meaning there are Wallmasters after you, so keep moving to avoid them and eliminate them when you need to. The door you opened earlier with the button switch is available, but is filled with invisible Skulltula and Keese. You can deal with them now (using your Fairy Slingshot is easiest) or come back when you have the Lens of Truth. The prize in this room in a Golden Skulltula hiding under the tombstone.
After getting the Map, enter the southeast cell. Shooting the crystal switch here will light the second torch and open the second door. If you play the Sun’s Song, you can get a red fairy spirit. The pots here also contain items you may be running low on.
Head towards the door you just opened and continue through to find three pots floating in mid air. Take a straight line to the first, break it and continue to the second. Break it, and make a turn straight for the third and final. Forward, break it and straight to the Small Key. Stick to the outer wall to make it back safely. Head back towards where you came into the well.
Near the entrance, the pool of water will now be drained. You can jump in and crawl through the hole on the east side. Up the mesh and through the door, which locks behind you, you’ll find a room with a bunch of diseased-looking hands reaching up from the ceiling. Approach one and it will grab you, prompting an attack from Dead Hand.
Let the hands grab you to draw him to the surface. Press A and/or B to get free, then get away from them. Now turn to the body and wait for it to get close. When it lowers its head, smack with your sword a bunch. If you wait too long, it’ll bite you. Keep doing this till it’s dead.
Defeat the Dead Hand and the door will unlock. He’ll also leave behind the Compass for you. How thoughtful. But wait, there’s more. Blow up the debris pile in this room for a small key underneath. The quick growing grass also provides items should you need it. Exit back to the main entrance.
Take the path around to the left again, but this time take the center west path. Jump down, walking under the underwater fence, and climb up the other side. Use one of your keys to open the door. Immediately, you’ll be ambushed by a Gibdo.
Defeat the Gibdo (it’s basically a Redead in mummy form, can be dealt with the exact same way). Head towards the back and you’ll encounter a Poe. Deal with it in the normal way, then look behind the pillar at the far end to find another Golden Skulltula. Lighting a Deku Stick and lighting the torches to open up the rest of the coffins only reveals more Gibdos, so you can leave this room.
Head to the northeast corner. Crawl through the hole here and you’ll find a barred door. Looking closely at the face on the wall, you can see just the tip of a Diamond Switch sticking out. Aim carefully and shoot it to unlock the door. Inside, Navi will tell you to watch out for Wallmasters. Deal with the Floormaster directly in front first, and use Jump Attacks whenever possible. (Using Jump Attacks prevents the Wallmaster from descending.) Alternatively, you can just run through, ignoring the enemies. Then use your second key and continue through the door.
Shoot the Skulltula’s off the wall, and bomb the debris to reveal a switch. Press it to open the hole in the very center. Go to it and jump down into the underground. Hit the button switch here, then jump down. In the big room take care of the Wallmaster because he’ll be a burden later. Then, head forward towards the single blue flame and take that tunnel down until you find a group of five Redeads. Play the Sun’s Song and eliminate them one at a time (or just walk past them while they’re frozen) to claim your Lens of Truth.
Finally, head back to the main room, avoid the boulders and acid, and take the northwest path. Using your Lens of Truth, spot the Invisible Skulltulas and eliminate them. At the end, you’ll find the final Golden Skulltula here. With all of your prizes in hand, take climb up the long ladders (get the Golden Skulltula in the first room you opened if you haven’t already) and exit the Well.