After filling your third Vessel of Light and becoming human again, go to the Howling Stone high on the cliff by Lake Hylia (where you couldn’t reach as a wolf). Explode the wall there that leads into a cave and go inside. Be sue to have a bunch of bombs and lantern oil. Bomb all the walls around the cave to find a ton of rupees.
When using the Flight by Fowl you’ll be able to fly around Lake Hylia with a Cucco and get rupees. Reach the Isle Of Riches, which can only be accessed by the Flight By Fowl. Each floor here has a special price. The following is a list of all the floors and their prizes:
Largest Floor: Nothing Second Floor: 10 Rupees Third Floor: 20 Rupees Fourth Floor: 50 Rupees Fifth Floor: Heart container Grand Prize (rotating floor): 100 Rupees
Leave Castle Town through the south gate. Climb the pillar on the left and reach the circle of rocks. Become a wolf and dig in the middle to drop into a cave filled with water and two small islands on each side. Kill the enemies to receive a chest and then knock down the bee hive for bait. You can catch big Greengills and Pike here as well as bags of rupees.
Go to Lake Hylia and play the bird game where you pop fruit balloons. Get everything at the beginning to get a perfect score ( 24 points). Then hit all twenty strawberries to receive a silver rupee.
Find the dog and bone near the Castle Town west gate. Throw the bone into the patch of grass to the right of the doctor’s house and sometimes the dog will instead bring back rupees. Repeat as many times as you’d like.
Go anywhere with lots of birds flying around, such as the bridge over Lake Hylia. Kill all the birds with arrows to make a number of rupees of various values fall to the ground.
Jump into the water in the center of Zora’s throne room with the Zora Armor on. Lift the small rocks at the bottom to find high value rupees. At least four or five rocks have yellow rupees(10), a couple have blue rupees(5), and one has a red rupee(20). Leave the throne room and come back to find more rupees. Repeat until your wallet is full.
Go to Death Mountain and say “Yes” to the Goron that asks if you want to climb on. Say “Yes” to the second Goron that asks you the same thing and look to the right. When you arrive, grab the rock and a red rupee will appear. Continue down the path and another rock with a red rupee will be there. Keep doing this as many times as desired.
Chop all the grass in the Fishing Hole to get rupees. You can find from 50 to 80 rupees and can repeat this as many times as desired.
Turn into a wolf right outside of Snowpeak Ruins. When you reach the snow, look to the right to see a ledge you can walk onto. Keep going up the path until you reach a plateau. Use your wolf senses to see many digging spots. Dig all the spots to get up to 50 rupees and a heart. Jump off an edge and repeat. The heart you find will keep you from dying so keep jumping off the ledge and collecting more rupees.
Go to the room in the Water Temple where you obtain the Boss key. In the uppermost section there are several pots. One pot has a blue rupee while three of them have yellow rupees inside. The rupees in the pots keep respawning so you can enter and exit the area until you have the desired amount of rupees.
Go to the Bridge of Elden. ON the other side from the own there’s a ladder. Kill the goblins there and move near the owl to jump across. There is an orange rupee there (worth 100 rupees).