Magical Laboratory Dungeon

This one is kind of specific. The players are magically transported to this dungeon, arriving in the central room. The floor of the dungeon is made from glass, through which the players can see water of indeterminate depth lighted somehow from below. Periodically, the players can see the guardian of this place swimming below the glass, observing them. The circular portal-looking things are hatches that can be opened (using switches or other means you decide) into the watery depths. Should the players decide to enter the water (which they must do to get to certain locations), will they encounter the guardian? Is it friendly or openly hostile?

Throughout this dungeon a story is told: a wizard and his wife were growing old and frail. The wizard decided to transfer their consciousnesses into the bodies of golems so they could live on and be together forever. However, after transferring his own consciousness, he was unable to transfer his wife's (for reasons you decide). She remains magically suspended in his lab while he attempts to solve the issue. Perhaps the players can bring him what he needs to finally transfer the wife's consciousness to the beautiful metal body he has made for her.