The Murray books (which start with "A Wrinkle in Time") are all excellent young adults' books, blending science fiction, fantasy and serious themes relating to the world in which we find ourselves. "Many Waters" is, in some ways, the most adult of the books. In some ways it is also the most fantasy-ful (I know that fantastic is the correct word, but it would be misunderstood) and also the most "factual", strangely enough.
L'Engle largely takes the antediluvian Bible history seriously, and seeks to envisage the world in which it takes place. Her answer isn't consistent with what many creationists would suggest, but it is coherent and plausible. She plumps for the theologically well-known idea that angels take a physical form, and are identifiable to the humans, and also explores the theologically solid idea that the two family lines - Cain's and Seth's - respond in very different ways to God.
The Murray twins find themselves having travelled back in time, and need to return home before they get caught up in Noah's flood. Superimposed on this plot, the story gently explores the idea of how a supposedly loving God could destroy the earth with a flood.