The landscape of the reservation and the surrounding area can be considered a main character itself, as the setting plays a subtle but vital role in the narrative. One of the most prominent themes throughout the novel is the examination of the dynamics between Western religion, like Christianity, and indigenous cultures. After all, Christianity was used as a weapon by conquistadors and Puritans to oppress North American indigenous peoples. There is a tense relationship between the former and the latter, despite various examples of intense devotion to faith.

The landscape and the tribulations faced by the characters, such as Novitiate Sister Cecelia, mirror the trials and suffering experienced by characters in the Bible. The rugged barren landscape of the novel parallels the Israelites' long trek through the Sinai desert. Even a flood that affects the main characters (resulting in the destruction of homes and many deaths) mirrors the Great Flood of the biblical tradition.

The other prominent theme in the novel is secrecy. The most pious people in the novel, ironically, have committed the worst sins. When these secrets are revealed, the religious cloth that they wear and the honorary titles that precede their names become neutralized; they have been reduced to flawed animals, like the rest of the people and wildlife in the barren landscape.