Requirements: Zelda's Lullaby, Song of Storms, Deku Sticks, Bombs, Hylian Shield
Hints
BEFOREHAND
Enter the future and head for the Windmill's interior at Kakariko Village. Show the organ-grinder your ocarina and he'll teach you the Song of Storms. Now return to the Temple of Time and replace the Master Sword, then go back to Kakariko Village. Play the Song of Storms inside the Windmill to make the pumps go so fast, the well will drain. You can now climb down the ladder of the well and walk through the dark passage to find yourself in the Bottom of the Well.
WELL, WELL, WELL!!
Walk along the narrow passages, knocking out the Giant Skulltula as you go. You'll come what looks like a dead end, but it's a fake wall. The skeleton near here hints to the Eye of Truth. Walk right through the fake wall to enter the main room. Keep going straight foward, jumping/swimming through water, until you come to another (fake) wall. Don't walk through the wall just yet, but turn left and place a Bomb on the pile of debris in the corner. A hidden passage down is revealed, where you can open a chest for some Bombchus.
Climb back up to the main room and go through the fake wall we missed before. Keep going foward to the two wooden planks crossed together in the middle of the room. You'll fall onto a platform with some Rupees, and you must now jump down to reach the rest of this room, called the pit.
Knock out the ReDead in this room, being wary of the toxic waste, and Bomb the boulders obstructing the passages. The boulders blocking the route with torches leads the way to the Map, guarded by another ReDead. Once you've found everything in the pit, return to the toxic waste and carefully walk along the wooden planks there to gather up three Silver Rupees. Now, climb up the ladder near the blue skull torch; the landing of this path up has another Silver Rupee, and when you climb up further you'll come to a room with the final Silver Rupee. The route back up to the main room from the pit is now cleared.
When you emerge through the previously blocked door, turn left and go through the fake wall to return to the main room. Now, see the main passage going left? Go along it, but hug the right wall. You'll go through a fake double wall and come to the large chest containing the Compass (don't go along the safe-looking floor, it's fake).
Go back through the double fake walls and to the corridor in the main room. Turn left and go around the corner, then immediately walk into the wall to get a Key. Go back through the fake wall, turn left and run to the other side of the room and go around the corner. Again, around this corner is a fake wall hiding another Key. When you emerge from this wall, head to the centre of the far north of the main room.
Here, you'll find a gargoyle statue which serves as a fountain. Play Zelda's Lullaby on the Triforce symbol here to drain the water. Now head west along the corridors, making the left turn along the visible passage and being wary of Giant Skulltulas as you go. Look out on your right for another turn-off, about half-way down. Go through here, opening the chest, and you'll emerge in a room with six coffins.
Using Deku Sticks, light the torches in the room to open all the coffins. Gibdos and bats will often emerge: just keep attacking the Gibdos to get rid of them, and make sure you have the Hylian Shield equipped in case the bats hit. Inside the other coffins are hearts and a Key. Return to the main room after sweeping the coffin room. Turn right and follow the passage. When you reach the south of the main room, you can jump into the dry pool which held some water. Open the chest, then go through the crawlspace.
In the next room, let one of the hands grab you to reveal your ugly opponent. Keep hitting all the buttons to get free before his attack connects, then lock onto him with Z-Targeting and attack with basic sword strokes when he lowers his head. Keep up the attacks, and eventually he'll cark it and yield the Lens of Truth. Use the Lens to reveal another chest here, containing 200 Rupees.
Now that you have the Lens, return to the north-west of the main room. Using the Lens to avoid the hidden pitfalls, place a Bomb on the rubble at the back of the passage to reveal a chest. Once you have the reward, work your way to the north-east of the main room to enter some more passages with more rewards.
The remaining keys are used up by going to the hidden area in the centre of the main room and using the Lens of Truth to open some small rooms.