Kakariko Village
Get in the windmill, play the Song of Storms for the musician, then get out and climb down the ladder leading to the well.
The Well
Get in the narrow passage, then go down the ladder. Get rid of the Skulltula, then go ahead, through the wall! You are in the main room, go ahead and go through the wall. In the middle of this room, where there is blood, there is an invisible hole. Go to the other side of the room while avoiding the hole and go through the opposite wall. Stand on the Triforce symbol and play Zelda's Lullaby, which lowers the water level. Then, turn around, go back through the wall, avoid the hole and go across the opposite wall.
You will be back at the start of the dungeon, but you can now access the pit in front of you. Jump, follow the narrow passage, get rid of the Skulltula, climb the wire fence and open the door. Now you have to beat a Dead Hand. Get close to one of the arms to make the Dead Hand appear, then when the arm lets you go, hit the monster. If you hit its head, one strike is enough! Then, you get the Lens of Truth in the chest. Use it right away to find another chest that holds a huge rupee.
Now you can look for the three Gold Skulltulas within the Well or play the Prelude of Light to get back to the Temple of Time, turn back into an adult and go on with your quest.