Carnivàle features LGBTQ+ characters like Iris Crowe, whose secret lesbian relationship highlights the repression and fear of the era, and Lila, the Bearded Lady, a strong, complex character with implied queer identity. Despite tragic outcomes for some, the series maintains an empathetic stance, framing societal prejudice and manipulation as external obstacles, thereby affirming the worth of these characters' lives and identities.

The series portrays organized Christianity, particularly through the antagonist Brother Justin Crowe, as a vehicle for manipulation, fanaticism, and immense evil. The narrative highlights the corrupting potential of religious power and dogma, positioning the audience against the oppressive and destructive actions carried out in the name of God.