There are old legends of a "witch of Wookey Hole", which are still preserved in the name of a stalagmite in the first chamber of the caves. The story has several different versions with the same basic features:

A man from Glastonbury is engaged to a young woman from Wookey. A witch living in Wookey Hole Caves curses the romance so that it fails. The man, now a monk, seeks revenge on this witch who—having been jilted herself—frequently spoils budding relationships. The monk stalks the witch into the cave and she hides in a dark corner near one of the underground rivers. The monk blesses the water and splashes some of it at the dark parts of the cave where the witch was hiding. The blessed water immediately petrifies the witch, and she remains in the cave to this day.^[61][62]

A 1000-year-old skeleton was discovered in the caves by Balch in 1912, and has also traditionally been linked to the legendary witch, although analysis indicated that they are the remains of a male aged between 25 and 35.^[63] The remains have been part of the collection of the Wells and Mendip Museum, founded by Balch, since they were excavated, though in 2004 the owner of the caves said that he wanted them to be returned to Wookey Hole.^[