Can be done in any dungeon. On an early floor, you'll encounter a Little Fairy who will give you an optional quest: "My home, not far away from here, is being occupied by a terrible Wraith. Can you help me it drive away?" I found the fairy on floor three multiple times.
Then, on multiple different later floors you will find a sparkling well. I always seemed to find it on 16, 26, 36, etc.
Fairy's Well "The well is surrounded by thick grievances, so it's hard for you to investigate. (Consume MP to dispel the grievances)" Disperse or Leave buttons
Pushing the Disperse button will drain ALL of your MP. My rough math is that you need to put approximately 2,000 MP total into the well to unlock it. You can do this over the multiple times you find the well.
After you've unlocked the well, it then says, "This well is surrounded by flowers in full bloom, full of vitality, but there are sounds of Wraith's mourning from the bottom of the well," and you can now enter.
There is one enemy in the well and a chest: Wraith, type undead 400 HP 40 base attack attacks each round 100% dodge
The chest gave three items: 1x three star, 1x four star, and 1x five star.
After you've cleared the well, on a later floor you will encounter the Fairy again and she will give you a reward, "Great! I can finally go back home! Here you are, please take these things!"
Reward: 5x Gems, one time only
On future runs, it only takes about 500 MP to unlock the well. You still have to kill the Wraith and you still get three items: 1x three star, 1x four star, and 1x five star. When you find the fairy again later, you get 100 EP.
tl;dr: put 2k MP into well over multiple floors, then get five gems on a later floor, one time only.