The show features incidental LGBTQ+ elements, primarily through satirical depictions of characters' ignorant or stereotypical views. While some characters express problematic opinions, the narrative generally satirizes these prejudices rather than endorsing them, resulting in a net neutral impact on the portrayal of LGBTQ+ themes.

Squidbillies features Krystal, a trans woman, as a recurring character. Her portrayal is largely problematic, with humor often derived from her trans identity through crude jokes, misgendering, and stereotypes. The narrative lacks affirming elements, presenting her identity primarily as a source of mockery rather than dignity or complexity.

The show consistently satirizes fundamentalist Christianity, depicting its adherents and institutions as hypocritical, bigoted, or foolish. The narrative uses these portrayals to critique specific cultural manifestations of faith rather than affirming its virtues, with no significant counterbalancing positive portrayals.