The Legend of Zelda: Skyward Sword HD, like most every other Zelda game before it, has got some lovely (now fully HD) bottles for you to find and keep your various potions and fairies in as you venture forth on your great quest.
With regards to this particular adventure, there are precisely five bottles in total for you to get your grubby mitts on. It's not many, all things considered, but a few of them are quite well hidden so it's probably best we provide you with their locations in this Skyward Sword HD Bottle guide, just in case you get stuck.
Zelda: Skyward Sword HD Bottle Locations
Bottle 1 Location: Skyloft - Bazaar
Once Link's adventure kicks off properly you can go get yourself over to the Bazaar in the centre of Skyloft and speak to Luv at the Potion Shop. Luv will have a quick chat with you at this point before she notices that you are sans empty glass receptacle. Being the lovely lady that she is, she'll then grant you your very first bottle for the princely sum of zero. Thanks, Luv!
Bottle 2 Location: Sealed Temple
The Sealed Temple is the scene for many of The Legend of Zelda: Skyward Sword HD's most intense cutscenes, it's also - even more excitingly - where you'll find empty bottle number 2. Grab it from the little wooden chest that's sat just to the right of the main stairs the first time you enter this area.
Bottle 3 Location: Skyloft
Sidequest alert! Yes, this bottle is obtained by doing a (mercifully short) side quest/errand that sees you rescue Orielle, who's stranded with a sick Loftwing on a small flat island that's located just beside Dodoh's Fun Fun Island.
In order to kickstart this questline, you'll need to speak with Orielle's brother, Parrow, who you'll find pacing nervously in Skyloft Plaza. Make sure you've got spare space in your inventory for the medicine Parrow will give you to aid his sister and, when the job is done, he'll let you keep the now-empty medicine bottle. Hooray!
Bottle 4 Location: Fire Sanctuary
Once you've acquired the Mogma Mitts in the Fire Sanctuary you'll need to backtrack to the first iron grate room you passed in the area - the first room containing one of those lava hands (Magnamos) that lifted you up on a stone platform. Use the Mitts to burrow down at the allocated spot to a new area beside this room where you'll find some Water Fruits that you can now use to kill the Magnamos in the grate room.
Doing this makes the lava in the area recede and grants you access to a new area below that leads outside to a platform containing a blue chest and your fourth empty bottle!
Bottle 5 Location: The Sky - Thunderhead
Our fifth and final bottle can be acquired from the Thunderhead region of The Sky once you've found and dealt a charged blow to Goddess Cube 26. You'll need to land on the island that's been automatically indicated on your in-game map and then burrow down in order to claim this last empty vessel.
Congratulations, you've now got the lot!
And that's the end of our bottle guide. Why not jump back to the Legend of Zelda: Skyward Sword HD hub area for more tips and help with the game?
There you'll find tips on the pros and cons of motion controls vs. analogue stick control, a list of the main differences between Skyward Sword on Switch and the Wii original, how to use the Zelda & Loftwing amiibo, where to find the Moonlight Merchant and the Thunder Dragon, and how to beat every boss and minigame.
You'll also find guides for all heart piece locations, all goddess cubes, and where to find every Gratitude Crystal, every upgrade treasure, every bug, and every potion recipe to fill your bottles with.