Many Waters, more than any other of L'Engle's fantasies, draws on Biblical and mythological allusions to tell an almost allegorical story. Besides the story of Noah and the flood, the novel uses the tale of Noah's grandfather, Enoch, who was taken into heaven, and references to fallen angels (nephilim) and heavenly messengers (seraphim).

Ancient legends of fallen angels mating with humans provide an important subplot. In addition, L'Engle borrows from classical mythology and folk tales to populate her world with unicorns, manticores, griffins, and shape-shifters.

Many of these characters and creatures are used to develop some of the novel's major themes. The unicorns, who can exist only when someone believes in them, are a test of the twins' growing faith. The novel, which examines the deceptive nature of appearances, uses the beautiful but evil nephilim and a gentle, but ferocious-looking griffin, to illustrate this point. At...