"God Only Knows" is frequently cited for referencing "God" in its title, a decision that Wilson and Asher agonized over, fearing it would not get airplay as a result.
Jim DeRogatis states that, as was common in psychedelic rock, the spiritual invocations in "God Only Knows" express non-specific sentiments which could be addressed to any higher force, and that it is "less of a prayer than a sensitive meditation about moving forward in the face of loss".