The Crystal Chamber is where Kashekim Nedakh, King of Atlantis, hid the Heart of Atlantis following the Great Flood. It is located deep below the city with the only access being through the King's Chamber.
Having had all knowledge of the crystal and the city's past erased so that history would not be repeated, the King was the only individual to know of the existence of the chamber. This was until Aziz accidentally wandered into Atlantis and spent two years secretly documenting its culture. How Aziz discovered the Crystal Chamber, its location, and how it could be entered remains unknown. Nevertheless, he recorded his finding in what would become the Shepherd's Journal.
Despite being hidden in the chamber, the Heart of Atlantis still managed to power the city enough to sustain life beneath the surface. It hovered over a bottomless pool of water, which is uses to hold at bay and become alert of any threatening figures from trying to retrieve it.
Since the events of Atlantis: The Lost Empire, the chamber appears to no longer be in use as the Heart of Atlantis now hovers over the city as it did before.