Not much is known about Lapis Lazuli's Gem life, except that she was trapped in a mirror and she insists that the Crystal Gems had some involvement in it. The lapis lazuli gemstone on her back is shaped like a water droplet, which coincides with her ability to manipulate water. At some point, her gemstone was damaged, impairing her abilities.
Ironically, the gemstone she is based off of dissolves in water.