Empty Bottles, one of Link's most precious resource as it can hold anything from a restorative potion, to a fairy. Seriously, these things are indispensible.
There are a total five empty bottles either hidden around the world of Hyrule and Lorule, or can be bought from variour merchants.
Here are the locations for all five empty bottles, as well as the necessary steps you'll need to take to obtain them. Keep in mind, some of them won't be available until after you get access to Lorule.
Empty Bottle 1
You'll find the first one in Kakariko Village, near the center where a merchant will be selling it for a 100 Rupees.
Empty Bottle 2
First you must have the Zora Flippers. Then travel to Lake Hylia, which is the lake to the South East of the map. Drop down and then swim North and then West towards where Link's house is. Once you swim underneath the bridge, you'll be able to clumb up and talk to the Bird Guy. Just tell him you like birds and that you came to chat with him and he'll give you an empty bottle.
Empty Bottle 3
Travel all the way Southeast of the map and head North. You'll see an empty bottle in the water that contains a message inside. Your task will be to go to Kakariko village to fill the bottle up with Premium Milk and then head to the mountain past Tower of Hera and deliver it to the Mountain Climber.
By now you should be able to fly to Tower of Hera using the Bell. Once there, head East. Make sure you have the Hookshot, otherwise you won't be able to go across the bridge. Head into the lava cave and drop down the moving platforms. Exit to the South and you'll find the stranded Mountain Climber there. Give him the milk and the empty bottle is yours.
Empty Bottle 4
Once you're able to go to Lorule, head to Link's house and bomb the back of it. Inside will be a chest that contains an empty bottle.
Empty Bottle 5
When you get to the Lorule Fairy Fountain, you'll notice that there is a crack near it. You'll need the Bomb Flower to open it. After that, donate 3,000 Rupees to the fairy and the bottle is yours.
