Numerous taphonomic studies show that archaeologists should carefully evaluate the origins of faunal remains found in archaeological sites. Although extensive research has been done on natural sources of terrestrial faunal remains in archaeological sites, much less has been devoted to potential sources of aquatic fauna. Hundreds of animal species feed on shellfish, fish, and other aquatic fauna, and many transport food to terrestrial landforms where they may be mixed or confused with faunal remains left by humans. In this paper, we illustrate the problem by summarizing the habits of a number of animals known to feed on and transport shellfish and other aquatic animals. We also discuss examples where the remains of aquatic animals of non-human origin may have been confused with archaeological materials. Such biological imprints may be most pronounced on early sites, where questions about the antiquity of aquatic adaptations are paramount.