The Crystal of Water, or Water stone, was one of the three Stones of Power that, when united, created the Crystal of Knowledge. It was a black crystal fragment with the Kryptonian symbol for water as well as transference.

The Crystal of Water was hidden on the planet Earth by a Kryptonian its discovery in 2005. It was inside an ancient statue of Mayan rain god in Honduras, Central America.

In 2005, Edgar Cole found the statue, discovered the Water stone and gave it to Lionel Luthor. Lionel intended to use it to switch bodies with Lex Luthor, but instead, Lionel accidentally switched bodies with Clark Kent. Clark was able to use the stone to switch himself and Lionel back. The crystal erased Lionel’s memory of the time he spent in Clark's body.

Edgar managed to get a hold of the Crystal of Water and gave it to Dr. Bridgette Crosby. When Jason Teague learned that Dr. Crosby had the stone, he killed her, stole it from her, and gave it to his mother Genevieve Teague. Lionel later blackmailed Genevieve into giving him the stone.

After Clark combined the Crystal of Fire with the Crystal of Air, the Crystal of Water was activated, downloading Kryptonian data into Lionel and simultaneously broadcasting a Kryptonian beacon that allowed Clark to find it. Lionel was rendered catatonic for weeks, having been transformed into a Kryptonian vessel for Jor-El to inhabit when needed. Clark combined all three stones and created the Crystal of Knowledge.