Unlike previous Zelda titles, Skyward Sword ditches the traditional four-bottle format in favour of… five bottles! Here’s a guide on the locations os all the Skyward Sword bottles.
First Bottle (Potion Shop)
You can get this bottle towards the start of the game after the opening sequence and you’ve gotten your green tunic. Go to the Bazaar section Skyloft, and into the potion shop. The owner will give you a free empty bottle to put potions in.
Second Bottle (Sealed Grounds)
Right after meeting the old lady at the Sealed Grounds, look around the room and you’ll find a chest with an empty bottle inside!
Third Bottle (Skyloft)
There are two side-quests you need to complete to get this bottle, but doing them doesn’t take too long. First, you’ll need to finish the lost child quest and then the missing sister quest (click on the links for detailed guides). As well as your gratitude crystals, you get an empty bottle for finishing these quests.
Fourth Bottle (Fire Sanctuary)
The fourth bottle is hidden in the Fire Sanctuary. It involves a little puzzling and running around so rather than explain it in words, this video I found below explains how to get the bottle well:
Fifth Bottle (Thunderhead)
This bottle is found in a Goddess Cube chest in the Thunderhead. To activate the respective Goddess Cube, go to the cave that leads to the Fire Sanctuary after the Eldin Volcano has erupted. There is a large pit of lava separating you from a grey stone slab with hylian symbols on it. A floating platform will allow you to reach the Goddess Cube. The exact location of the chest with the bottle inside is on the map below: