Moon snail predation on clams is a common model system of predator–prey interactions. In this system, the predator bores through the shell of its prey, leaving a distinct and identifiable hole. Some paleoecological and behavioral research on moon snails suggests a trend in predation preference directed toward clams with small shells. Rarely, however, have studies tested relative drilling frequencies across species and size ranges in natural assemblages of clam communities. We examined the clam community composition at two beaches in South Carolina, USA, and we then tested moon snail predator preferences for (a) clam prey species and (b) whether their selection is related to prey shell size. We collected a total of 1,879 clam shells, identified each shell to species and recorded their anteroposterior length. The species composition of clams differed significantly between the two beaches; Anadara ovalis was dominant at both sites, but three of ten total species were only collected at one beach. Folly Beach had nearly a 60% higher the overall drilling frequency (34.6%) versus Edisto Beach (21.8%), and this may be linked to the differences in clam community compositions at the sites. For A. ovalis and Mulinia lateralis, shells with larger lengths have lower probabilities of being bored by a moon snail. Anadara brasiliana, which generally is a thinner‐shelled clam species, had the highest total drilling frequency (77.2%), and Noetia ponderosa, a thicker‐shelled clam, had a considerably lower drilling frequency (12.0%). We conclude that both community level factors (species composition) and population characteristics (shell size distributions) may influence the local drilling frequency by moon snails.