After you clear the Great Bay Temple and travel through Ikana Valley, the next and final dungeon is in Ikana Canyon to the east.
Reach the Upper Canyon
In this area, if Tatl signals to you, it means that there is a ninja nearby. You can wear the Garo's Mask to make the ninja appear, then use your shield to defeat the ninja and it will give you a hint before it disappears.
In the lower part of Ikana Canyon, if it's daytime, you will see Sakon prancing around. You can talk to him and agree to show your sword. Tatl will prevent Sakon from stealing it, and you will find out from Sakon that if you can make the river flow again, the ghosts will go away from the Music Box House.
Go to the bridge over the water and freeze the two Octoroks. Jump over them to reach the other side of the bridge. Then use the hookshot on the tree to the left. There is another tree up above. Use the hookshot on it. Then use the hookshot on the tree above that. There is an owl statue next to this third tree. Hit it with your sword to activate it.
Revive the River
Go past the Music Box House, following the dry riverbed. You will reach a cave in the north wall. Go in. Walk into the middle of the pool, and Sharp will appear. As soon as you can, play the Song of Storms. (If you don't know it, read the Learn a New Song section on the previous page.) After you play the Song of Storms, the curse on the river is lifted. Watch the cut scene.
Get a New Mask
Go outside and put on the Stone Mask. If you don't have it, read the Get the Stone Mask section the previous page. While wearing the Stone Mask, go into the Music Box House. If you accidentally scare the little girl into the house, put the Stone Mask on and put a bomb outside of the house to make her come out again. Inside the house, go to the left and go downstairs. Turn around and walk to the big colorful closet. After the thing comes out, play the Song of Healing as soon as possible. If you don't play it soon enough, you'll get kicked out of the house. If that happens, put a bomb outside while wearing the Stone Mask to make the little girl come outside. Then go in and try again. After you play the Song of Healing for the mummy that comes out, there is a cut scene where Pamela reunites with her father, and you get the Gibdo Mask.
Go Beneath the Well
The next destination is the empty well that is southwest from the Music Box House. However, inside you will find Gibdos who won't let you pass unless you give them certain items. Here are the items that you should acquire before you enter the well: five magic beans, a fish, ten deku nuts, ten bombs, and some milk.
You can buy magic beans for ten rupees each from the Business Scrub in the Southern Swamp who lives next to the Swamp Tourist Information Center if you talk to him while wearing the Deku Scrub mask. You can catch a fish in the kitchen of the Stock Pot Inn. You can get Deku Nuts from the item shop in West Clock Town, or you can get them for free by killing Deku Babas that don't stick straight up in the air. You can find Bombs in the item shop as well, or you can just cut bushes in Termina Field until you find some. You can get cheap milk from the Gorman brothers at the Gorman Racetrack in Milk Road (but only if Epona is not with you), or you can get free milk by playing Epona's Song for a cow. To find cows, go into the hollow log between Clock Town and Southern Swamp, then use a bomb in the middle of the log to reveal a hole. Fall into the hole to find the cows.
In the well, there is also a fairy fountain that you can reach if you have a blue potion, but I don't think it's worth the effort.
When you are ready, go beneath the well.