A central theme in any detective work is suspicion and the attempt to find out who is at fault for the crime committed. This novel sets the standard trope of multiple characters with vague excuses and alibis, as many of the characters both act erratically and find themselves unable to explain their actions or whereabouts. The novel traces the different characters' stories, providing various narrative perspectives in order to tease out the truth about what happened to the stolen diamond.

Tying in very closely with suspicion is the idea of characters holding deep secrets—a now standard them in detective fiction. The culprit, Godfrey Ablewhite, holds a secret that is initially unrelated to the Moonstone but ends up being the reason behind the crime—that he had embezzled all the money he had put into a trust fund for heirs. He planned to use the stone to repay his debts now that the fund was about to become mature. Additionally, Rosanna, who is a maid in the house, acts strangely before committing suicide. It is revealed that she was not the criminal but held a secret love for Franklin, who proposes to Rachel; that was the reason for Rosanna's erratic behavior.

Many works of detective fiction, including The Moonstone, involve romantic entanglement. The eighteen-year-old Rachel has multiple suitors who are trying to win her hand in marriage. While trying to navigate the complexities of the crime, the characters also try to figure out the various romantic entanglements that are going on around them and to determine who is the appropriate suitor for Rachel.