1.Dragon Roost Island
When you first arrive on Dragon Roost Island, you will be told to speak with Medli. After you speak with her, she will ask you to meet her outside.
Find Medli outside on the path leading to Dragon Roost Cavern. Speak with her to help her enter Dragon Roost. Pick Medli up and walk to the elevated rock nearby, and when the wind is blowing towards the ledge, throw her Once Medli lands on the edge, she will thank you and give you the first Empty Bottle.
Sail to Bomb Island. There is a submarine south of the island. Enter the submarine and defeat the three Bokoblins inside to reveal a treasure chest that contains an empty bottle.
3.Rock Spire Isle
Sail to Rock Spire Isle. Enter the “Masked Beedle” shop sailing around the island. You can purchase an empty bottle from the shop for 500 rupees.
This bottle cannot be obtained until after you have defeated Helmaric King in the Forsaken Fortress.
This bottle can only be obtained at night.
Speak to Mila, a poor girl who stands near a tree between the Chu Jelly Juice Shop and the Hall of Wealth; she will tell you to leave her alone. Run down the nearby stairs, and Mila will begin walking in the opposite direction.
Then, turn around and follow Mila at a distance. Make sure that you do not get too close to her (and making sure she cannot see you). If Mila sees you, she will run away and the sidequest will reset until the next night. When Mila begins picking Zunari’s safe, walk up behind her and speak to her. Select the first option for all of the questions that she asks. If you answer correctly, Mila will give you an empty bottle.