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A mini-dungeon does not consist of a whole dungeon but contains some elements of a dungeon. Hidden Holes are not considered mini-dungeons. Mini-dungeons usually must be completed as part of the storyline. Hidden dungeons do not count as mini-dungeons because they are not necessary to complete the game.
The Ice Cavern holds the Iron Boots that can be obtained after fighting the White Wolfos. The "Serenade of Water" is also learned here. It is located in Zora's Fountain, but is only accessible when Link is an adult, when the entire Zora region is frozen. It is also where Link can obtain Blue Fire which he can store in a Bottle and is the only place besides the Inside Ganon's Castle where he can obtain it for free.
The Bottom of the Well holds the Lens of Truth, and the mini boss Dead Hand, but no Heart Containers or Pieces of Hearts can be found. The well is located in the heart of Kakariko Village and is only accessible when Link is a child and after he has drained the Well by playing the Song of Storms in Kakariko Windmill.
The Gerudo's Fortress contains several Gerudo that act as mini-bosses and defeating all the Gerudo Thieves and freeing the Carpenters earns Link the Gerudo Membership Card from Aveil, which is required for Link to progress to the Haunted Wasteland, Desert Colossus, and Spirit Temple.
The Moblin's Keep has no item or Heart Container, but the Great Moblin is fought there. Interestingly, upon the defeat of the Great Moblin and the destruction of the keep, Link finds a Piece of Heart in the ruins. The Moblin's Keep is located in the Great Moblin's Realm, just west of Sunken City.
The Forsaken Fortress holds the Skull Hammer, a Heart Container, and a boss, the Helmaroc King. However, this dungeon is visited two times, and the first does not feature an item. It is located at the extreme north-west region of the Great Sea.
The Savage Labyrinth has no item, Heart Container, or boss, and is found on Outset Island. It has fifty floors, each with all various enemies, increasing with difficulty as Link descends. At the thirtieth floor, there will be a Triforce Chart, necessary to find a piece of the Triforce of Courage. After obtaining the Mirror Shield, Link can travel down further to the final twenty levels. At the absolute end of the Savage Labyrinth is a Piece of Heart.
Also Ice Ring Isle and Fire Mountain are also considered mini-dungeons. This is due to them not having a boss, nor many rooms, but containing the Iron Boots and the Power Bracelets respectively, both important items necessary to complete the game. There are also time limits to complete them, creating a difficulty setting.
The Cave of Ordeals has no item, Heart Container, or boss. It has fifty floors, each with several enemies that get harder as Link descends, similar to the Savage Labyrinth. Every ten floors the Great Fairy appears and releases fairies at each Spirit's Spring. The prize at the end is Great Fairy's Tears, a cure-all substance. The Tears can then be found at any of the fairy springs around Hyrule. It is located in the Gerudo Desert.
In Twilight Princess HD, there is a special mini-dungeon called the Cave of Shadows which can only be accessed via the Wolf Link Amiibo. The mini-dungeon is unique in that Link is stuck in his Wolf Link form while inside the dungeon itself. Completing it grants Link a new Wallet upgrade (if he has the Giant's Wallet he will receive the Colossal Wallet which allows him to carry 9,999 Rupees).
The Waterfall Cave has no item, Heart Container, or boss. However it is filled with enemies and Link must pass through it in order to free his Crimson Loftwing. Link is also required to obtain the Practice Sword in order to access it. In many ways it is a mini-dungeon that acts as a tutorial for combat and dungeon-based exploration.
The Pirate Stronghold has no item, Heart Container, or boss. It has a central puzzle involving a Timeshift Orb. Link must carry the orb throughout the entire dungeon in order to solve its puzzles. When Link finishes the mini-dungeon, he gains the ability to dowse for the Sandship.