After completing the Water Temple, head over to Kakariko Village. As you approach the area of the village in which the windmill is located, you will see flames. As you go closer to the well, Sheik will appear. Sheik will teach you another Ocarina Song. Around this time, something will escape from the bottom of the well. Sheik then tells you to find the Lens of Truth. To do this, you must first learn the Song of Storms (see the "Ocarina Songs" summary for more information on this). After you learn this song, return to the Temple of Time and put the Master Sword back in its pedestal. You will now be a child. As a child, go to Kakariko Village and play to Song of Storms in the windmill. When you do this, the windmill will pick up speed and draw up all of the water from the well.
Once the well is empty, you can climb down the ladder to the bottom. You will now enter the Bottom of the Well. As you proceed forward, it seems that you are blocked by a wall. Not so. Walk into the wall and you will end up walking right through the wall to the rest of the level. This level is full of fake walls and hidden holes in the ground that drop you to the lowest basement. You cannot see any of these things until you obtain the Lens of Truth, which is somewhere in this level. Before you find this lens, you have to be very careful and remember the places where you might have fallen through some hidden hole in the ground. There is one boss here. He is in a room that has eight arms growing out of the ground. If you walk near an arm, it will grab you and hold you. When this happens, the boss will appear and begin to walk towards you. You have to break free of the grasp of the arm, and then wait until the boss stops in front of you and lowers its head. His head is his weak point. Once his head is low enough for your sword to reach, hack at it. The boss will then run away and disappear.
To make him reappear, you must let another arm grab you and hold you. Repeat this procedure until the boss is defeated. When you obtain the Lens of Truth, you can set it to one of your "C" buttons. When you use this lens, it will consume magic - so use it sparingly and do not forget to "turn it off" when it is not in use. There are some places that you will notice, if you have your compass, that there should be a treasure chest there. Use the Lens of Truth to reveal the treasure chests. In addition, some hidden treasure chests are very close to visible ones, so it might be hard to see on your map that there are two treasure chests in a location. To alleviate this, always use the Lens of Truth near visible treasure chests - you may find that there are other ones nearby.
Once you have cleaned all the treasure out of the Bottom of the Well, leave and continue with the rest of your quest. The next to temples, the Spirit Temple and the Shadow Temple, can be tackled in any order that you choose. This walk-through will first deal with the Spirit Temple, which is in the next section...
Proceed to Spirit Temple...