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[Joaish (RedTribeLink)]

Apologies for the late response, but here are the locations of all five crystals:

 

Spoiler

1. Solving the ice block puzzle in the western most part of Shivering Shaft

2. Defeating all enemies 2 rooms south of the Ice Rod room in Shivering Shaft

3. Use the metal spring in the most northern part of Coral Cave (left of the Shivering Shaft entrance)

4. In Dirtroot Den, on the secluded part on the screen with the Dodongos (needs any way to cross water)

5. Swim down the waterfall in Coral Cave that goes down to Hollow Hole to reveal the crystal (this is probably the one you're missing as it's spawned via a combo)