After you get the Gibdo Mask and learn the Elegy of Emptiness in Ikana Castle, you can complete the switch puzzles in the Stone Tower area.
Reach the Stone Tower Area
The door to the Stone Tower area is between Ikana Castle and the cave where you played the Song of Storms to make the river flow again. Go up the statue's tongue to enter the Stone Tower area.
Reach the Top
Go straight ahead and hop over the three floating platforms. Stand on the button straight ahead, then play the Elegy of Emptiness to make a statue to stand on the switch. Then look to the side to find a hookshot pillar. Use the hookshot on it. Throw a bomb at the Beamos to kill it, then step on the switch. Put on the Goron mask or the Zora Mask and play the Elegy of Emptiness to put another statue on the button. (If you play the Elegy of Emptiness while still in Link form, the first statue will disappear, which you don't want.)
Then look to the side to see a hookshot target slightly higher up. Use your hookshot on it, then step on the switch there and wear either the Goron or Zora mask (whichever one you didn't use on the second switch) and play the Elegy of Emptiness to make a third statue. If you did it correctly, there should now be three stone blocks nearby that you can jump across. Go across them.
On the other side, don't step on any of the switches. Instead, use the hookshot on the target that is on the level above you, then put a statue on the switch there. Then look for another hookshot target that is on the level above, and when you get up there, bomb the Beamos, then put a statue on the switch. Then do this one more time until you have three statues on the switches on this side. There should now be three stones straight ahead that you can hop across. Go across them.
There is a second set of three side-by-side switches up here. Ignore them. Use your hookshot on the target up above. Then get down and go to the south edge of this platform, and use your hookshot on another target up above. Then look up to find a third target. Use it, then walk over to the owl statue that is here. Hit it with your sword to activate it.
Enter the Temple
The entrance to the Stone Tower Temple is behind you. To reach it, you have to put statues on the three switches here, but you have to do so in a specific order. But before you do that, you may wish to play the Song of Time to go back to the first day, then play the Song of Inverted Time (i.e. play the Song of Time backward) to slow the flow of time, then warp back here.
Put the statues on the switches like so: if you are facing the Stone Tower Temple, put a statue on the switch on the right. Next, put a statue on the switch on the left. Finally, put a statue on the switch in the middle. Then you can go into the Stone Tower Temple.