Mt. Crenel Business Scrub
The first bottle can be bought from the Business Deku at the foot of Mount Crenel.
Down the Chimney
As mini-Link, go down through the chimney of the Rupee store, and take that bottle. Feed the food to his dog, and you have another empty bottle.
Fuse a kinstone with your grandfather, and open the chest that appears, inside is the third empty bottle.
Fuse the Kinstones with the mysterious walls throughout Hyrule to make the Gorons break through the cave. At the very end of it, you will find a chest containing the last empty bottle.