The Legend of Zelda: The Minish Cap - Bottles

Trilby Highlands Bottle: This bottle is obtained by default, as part of the game's storyline. It's pretty easy to get. From the Hyrule Castle Town, head north and go over the bridge to the west into the Trilby Highlands. From there, keep running south until you find a ladder, it's pretty hard to miss. Climb down it into a cave. Bomb the wall inside, and head through the passageway. There will be a Deku Scrub inside, deflect the projectiles he fires at you back at it with your shield. After that, talk to the Deky Scrub and he will offer you a Bottle for the price of 20 rupees.

Eastern Hills Bottle: This bottle is also really easy to get! You will need to have gotten the Kinstone Bag. Go to your house and fuse kinstones with your grandfather. A chest will appear outside near the house, open it and you'll find another bottle.

Lake Hylia Bottle: You will need to have completed the Cave of Flames before you can get this bottle. Go into the Hyrule Town, and enter the house to the south (the yellow one with the cup of coffee on top of it). Use the Cane of Pacci on the large blue vase inside, and shrink down to Minish size. Go up the small set of stairs and follow the passageway out of the building. Once outside, cross the wooden plank to go over to the town shop. Inside the roof of the shop there will be a bunch of monsters, avoid/kill them and make your way to the upper right hand corner of the roof and head down the stairs. Use the vase to get back to your normal size, and pick up the bottle. The shop keeper will notice you, but will let you keep the bottle as long as you feed his dog. He will mark the location of his Lake Hylia house on your map. Go to the house and use the bottle to pour out the dog food for the shop keeper's dog to eat. From there you can keep the empty bottle!

Eastern Hills Bottle #2: This bottle is the reward for finishing the Goron Quest.