Empty bottles are used to transport potions and other things like fairies. In total you can find five that you can store in your Adventure Pouch.
Empty Bottle #1
Location: Skyloft, Bazaar
You get this Empty Bottle for free when you talk to the potion brewer in the bazaar for the first time.
Empty Bottle #2
Location: Sealed Temple
The second Empty Bottle is in a small chest in the Sealed Temple. This chest is in the right, back corner and the Empty Bottle already contains a Revitalizing Potion.
Empty Bottle #3
Location: Skyloft
After receiving Gratitude Crystals for the first time, you meet Parrow in the village square, who is missing his sister Orielle.
He tells you that she made her way to a colorful island in the southwest. Now fly towards the Fun Fun Island, on the way you will find Orielle on an otherwise empty island. Her bird is injured and she asks you to get medicine from her brother. So fly back to Parrow, who will now give you a new Empty Bottle with mushroom spores. Note: If you already bring mushroom spores to Orielle with one of your own bottles, you will still receive an Empty Bottle from her brother as a reward.
Empty Bottle #4
Location: Fire Sanctuary
This Empty Bottle is available in the Fire Sanctuary. Once you have received the
Mogma Mitts, return to the first round room where one of the Magmanos has already attacked you.
At the top of the bird statue there is a tunnel that you can dig into and where you can open a grate.
Behind it you come to a room with water plants. Impale one of them to defeat the Magmanos, which opens a passage to a chest.
Empty Bottle #5
Location: Island north of Insect Island
In the Volcano Summit there is a Goddess Cube in the middle of a lava flow that leads to the dragon’s lair (artifact Eldin #9).
Activates this artifact, the corresponding chest is located in a rock north of Insect Island.