Kakariko Merchant (Hyrule)
A street merchant in Kakariko Village will sell you a bottle for 100 rupees.
Under the Bridge (Hyrule)
After you obtain Zora’s Flippers, swim under the large white bridge east of Link’s House. Speak to the man who lives under the bridge to receive a bottle.
Message in a Bottle (Hyrule)
There is a bottle floating in the shallow waters on the east side of Lake Hylia. There is a message inside the bottle: the writer is lost on Death Mountain and wants some premium milk from the milk bar in Kakariko Village.
Visit the milk bar in Kakariko Village and speak to the man behind the counter to receive the premium milk.
The man who wrote the letter is lost on Death Mountain near Rosso’s ore mine. To reach him, travel over the bridge east of the Tower of Hera and enter the cave. Wooden signs guide the path to Rosso’s ore mine, but do not follow them.
The cave is full of lava and requires that you fall on to moving platforms with proper timing. When you reach a large platform with a wooden sign telling you to travel east to reach Rosso’s ore mine, ignore the instructions and travel south instead.
Continue to follow the path of moving platforms until you reach the exit. Outside, use merge and walk east to another ledge to find the lost man. He will drink the milk and leave you the empty bottle.
Vacant House (Lorule)
There is a vacant house directly south of Lorule Castle (this house is Link’s House in Hyrule). There is a treasure chest inside the house that cannot be reached by walking through the front door. Instead, place a bomb on the back wall of the house to create a second doorway. Enter the house from the new doorway to reach the treasure chest and receive a bottle.
Great Rupee Fairy (Lorule)
The Great Rupee Fairy’s fountain is hidden behind a large cracked stone northwest of the Big Bomb Flower in Thieves’ Town. Use the Big Bomb Flower to destroy the stone and enter the fountain.
Inside, donate rupees in increments of 50 or 200 until you have donated a total of 3000 rupees (this can be done in one visit or added up over multiple visits). When 3000 rupees have been donated, you will receive a bottle as a reward.