1) Tribly Highlands
Required Items: None

The first bottle is very easy to find, and in fact, it is required that you get it. First, make sure you have some rupees with you and head to the Tribly Highlands by taking the west exit of Hyrule Town. After you exit Hyrule Town, go a bit to the south and enter the stairs you find. Once inside you will find a large block to your left, and a cracked wall to the right. Place a bomb in front of the cracked wall to enter the next room. Inside you will find a Deku Scrub, and simply deflect the nuts he fires at you with an equipped shield. Once you return his fire and sucessfully hit him, apporach him and talk. He will sell you a bottle for 20 rupees.

2) Lake Hylia
Required Items: Cane of Pacci

Once you have completed the second temple, the Cave of Flames, return to Hyrule Town. Visit the store in the south of town and you should notice a bottle behind the counter. You can't get this bottle yet, so head back outside and head towards the inn. Enter inside the inn and use your Cane of Pacci on the blue vase inside. Then use the vase to shrink down to minish size. Head to the back of the inn and walk up the small stairs. Once you have gone up the stairs, walk over the drawers towards the small hole in the upper left corner. Enter the small hole and walk across the wooden planks until you exit the inn. Cross the plank between the two houses and either avoid or kill the monsters there. Enter the store. Once you're inside of the store, use the vase to return to normal size. Take the bottle and talk to Stockwell, he will give it to you for free as long as you feed his dog for him. He marks a location on your map, which is by the east exit of town, after Lon Lon Ranch. Make your way to the house and once you find it following your map, go inside and walk up the the dog's food bucket. Approach the bucket and check it, and you will pur some food inside. You are now able to use the second bottle.

3) Eastern Hills
Required Items: Kinstone Bag

To get the third bottle, begin by returning to your house and talking to your grandfather, master Smith. You now have the ability to fuse kinstones with him. Once the fusion is complete, a chest will appear in the Eastern Hills, go find the chest and the third bottle is easily yours.

4) Lon Lon Ranch
Required Items: Kinstone Bag

See Goron Quest