Great Fairy Fountains are the only locations in Hyrule where Link can upgrade his armor. Unfortunately, no one in the game is very forthcoming on how to upgrade armor, so you'll have to find this out mostly on your own.
There are four Great Fairy Fountains in The Legend of Zelda: Breath of the Wild, but assistance from the Great Fairies in Zelda: BoTW won't come cheap. These Great Fairy Fountains must be unlocked with cold hard rupees, and only after getting paid will the fairies within provide Link with armor upgrading assistance.
How do Great Fairy Fountains work?
Once you find a Great Fairy Fountain, the locations of which you can find below, you'll need to pay a certain amount of rupees before the Great Fairy within will assist you. The fee to unlock the fountains goes up with each one you unlock. The first fountain will cost a paltry 100 rupees, the second will be a more significant 500 rupees, the third fountain opened will cost you 1,000 rupees, and the fourth is a whopping 10,000 rupees. Once unlocked the Great Fairies at the fountains will offer armor upgrading services.
How to upgrade armor in Zelda: Breath of the Wild
Each Great Fairy Fountain you unlock allows you to upgrade a piece of armor by one star. The first upgrade will add a small defense bonus, but the real usefulness of armor upgrading comes when you upgrade a complete set of armor to at least level 2.
Certain sets of armor, when all pieces have been upgraded to at least level 2, give special effects that can provide beneficial status effects to Link. Check out our Armor Set list to see specific benefits armor sets provide when leveled up.
Great Fairy Fountain Locations in The Legend of Zelda: Breath of the Wild
Finding a Great Fairy without assistance can be a pain. The Great Fairy Fountains are off the beaten trail and easy to miss. NPC characters will give you clues for some of the fairy fountains, and at least one of them you'll probably be led to during the main quest. There are four Great Fairy Fountains in Zelda: Breath of the Wild, plus one bonus Fairy Fountain where you can meet a very strange and powerful being.
Tabantha Tower Region Great Fairy Fountain - Great Fairy Kayasa
To get to Kayasa's Great Fairy Fountain, warp to Tabantha Tower. Once there, head south to the base of Piper Ridge. Check your map for the small pool of water, and you'll find your target.
Akkala Tower Region Great Fairy Fountain - Great Fairy Mija
Mija's fairy fountain is found due east of the Akkala Sheikah Tower. In a small forested area on the eastern bank of Lake Akkala, you'll see a pool of water. This is where Mija's Great Fairy Fountain is located.
Kakariko Village Great Fairy Fountain - Great Fairy Cotera
Cotera's Great Fairy Fountain is likely to be the first you run into. The fountain is located on the path that runs beside the shrine north-northeast of Kakariko Village. Just look for the small pool of water in the northern part of the forest, and you'll find Cotera's Great Fairy Fountain.
Gerudo Wasteland Tower Region - Great Fairy Tera
Tera's Great Fairy Fountain is a bit harder to locate since it doesn't have the telltale sign on the map of a small pool of water. To find this fairy fountain you'll need to go to the Dragon's Exile area of the Gerudo Wasteland. You'll locate the skeleton of a dragon there and near the tip of its tail is Tera's Great Fairy Fountain.
How to Find the Great Horse Fairy
There is a fifth Great Fairy in Hyrule, though she has nothing to do with armor upgrading. To find the Great Horse Fairy Fountain you'll need to go to the Lake Tower Region of Hyrule. Look on your map for the Lake of the Horse God, and at the end of the path leading past the lake, you'll find the Great Horse Fairy Malanya. Malanya has the unique ability to resurrect any of the horse you've registered that has perished during your adventure. So, if you had an equine friend that you've lost, you could bring them back. However, Malanya also requires patronage, and you'll have to pony up 1,000 rupees before she'll provide her services.