Just like almost all previous Zelda games to date. The Wind Waker has several bottles found throughout the land. Below is a listing of all four found in the game with locations, what you need to get them, as well as your reward.
Location - Dragon Roost Island (F2) Required Items - None How to get - Medli gives it to you after throwing her to the dungeon entrance. This bottle is the onle one that is mandatory to complete your quest.
Location - Bomb Island (F5) Required Items - None How to get - Find the man with a telescope just south of Bomb Island. The man is looking at a submarine through his telescope. Use your telescope or follow his sight to find the submarine. Head inside and defeat all the enemies in here to grab the second bottle.
Location - Rock Spire Isle (B3) Required Items - None How to get - Head to Beetle's shop and you can purchase the bottle for 500 rupees.
Location - Windfall Island (D2) Required Items - None How to get - You can get this after defeating Helmorac King at the Forsaken Fortress. At night, find the poor girl Mila and she'll tell you to buzz off. Go to the stairs and she'll run away. Follow her, but be careful. She turns around to look periodically to see if you are still following her. Keep your distance from her and hide behind items when she looks back. After getting to Zunari's safe, talk to her. Choose the first selection for each question she asked. Since you caught her trying to steal from the safe she will give you the fourth and final bottle.