In the game there are four possible bottles. All four bottles are found in the Light World of Hyrule.

Empty bottle
Red Potion
Green Potion
Blue Potion
Faerie in a bottle
Bee in a bottle

1. The first bottle is located in Kakariko Village, in the Light World. It is in the north-northwest part of Hyrule. This bottle is purchased for 100 rupees. You buy it from the man that is sitting on top of a carpet.

2. The second bottle is also located in Kakariko Village, in the Light World. In the tavern located in Kakariko village. It is in the southwest part of the village. It is the long building. Go into it and you will see a treasure on the other side, but you cannot reach it. Just go back outside and walk around to the other side of the long building. There is a secret entrance. Just walk into the building from the top of it and you will be on the other side of the tavern. Open the treasure to get the bottle.

3. The third bottle is a little hard to find. It is located just east of your house in the Light World. From your house go left a screen. The actual bottle is located under the bridge. Go above the bridge and walk to your right. Keep walking until you find a place where you could jump into the river. Once you are in the river swim back towards the bridge and eventually under the bridge. You will see a man under the bridge. Talk to him and you will get the third bottle.

4. The fourth bottle is the hardest to get of them all. You will have needed to get your sword tempered before you can get this bottle. In the Dark World, go to the place where you got your sword tempered. It is just east of the Village of Outcasts. Where the house use to be will now be a run down place with a treasure chest there. Go next to the treasure and it will start to follow you. Go back into the main part of the Village of Outcasts with the treasure chest following you. You cannot jump down anything or the treasure chest will stay behind. Go south of the village of outcasts. Keep going down and then right. Make your way all the way to where your house would be if it were the light world. From where your house would be, go south and then south, and keep going until you have reached the southern part of Hyrule. From where the second crystal is located head left. Keep going until you change screens. Then use the mirror and go into the Light World. From here go up a little and talk to the guy that is sitting next to the sign. Before you wouldn't be able to understand you but now he will unlock the chest for you and you will get the fourth and final bottle.