When the Scrub attempts to return to his nest, he will walk right into you. 2 Defeat the Scrub in this room by deflecting the Deku Nuts he fires back at him with your Deku Shield (the Slingshot doesn’t work, he just retreats back into the ground). Use the ivy wall in the northwest corner to climb back up. Kill the second Gold Skulltula, and climb up the wall to claim the token.
Use your Fairy Slingshot to kill the Gold Skulltula on the grating on the eastern side of the room. Skulltula Tokens can be redeemed at the House of Skulltula in Kakariko Village for rewards. Some rewards are good, some are just plain awful. On the other side of the low wall, there are a number of stone blocks to the left. Enter the shop (it must be daytime to work), and go through the passage on the left side of the store to reach the grotto behind the buildings. Climb back up onto the southeast ledge once more, and open the chest behind the lantern to find a Recovery Heart. Step on the switch next to the lantern. Step on the switch to activate the lantern. Step on the switch again, and this time use the platforms to reach the small alcove in the northern part of the room.
Swim over this button, then press and hold down A to swim down and touch the switch. He will then open both of the doors in the room, and give you a useful hint for avoiding fall damage (press forward on the joystick as you land). You’re now going to have to jump off the edge and land on the bit of webbing, clear down on the first floor of the Trunk. Remember to use the Biggoron Sword if you have it.
Begin circling the room in the opposite direction so that you intercept it halfway around the room, and use a jump attack to deal damage to it (use a regular strike if you have difficulty timing the jump attack). Unfortunately, if you have been skipping out on it then you’re going to miss a Deku Nut upgrade and 500 easy rupees. If a Biri gets too close, use a Deku Nut to stun it. As always, use the Biggoron Sword if you have it. To access the fountain, you have to have the Gold Gauntlet. The Gold Skulltula hangs halfway up the ivy wall. Face the long ivy wall that you fell down to reach this area, on the south side of the room. Ignore the Big Skulltulas who drop down, and keep going to the left until you reach a door.