Bottle #1:At Lon Lon Ranch, play Talon's Super Cucco Game. When you win, you will receive a bottle(1) with Lon Lon milk

Bottle #2: In Kakariko village, find all the cuccos and return them to the pen, then talk to the lady standing next to the pen, she will give you a bottle.

Bottle #3: At Lake Hylia (you must have the silver scale), dive into the water to find a bottle and a letter.

Bottle #4: As adult Link, go to the market and talk to the ghost person in the house directly to the left asyou enter. Go outside and collect poes, once you collect 1000 points, the ghost will give you a bottle.