We tested for the influence of gender, stream, and urbanization on morphological variation in rusty crayfish (Orconectes rusticus) in an east-central Indiana, US watershed. We used geometric morphometrics to characterize shape and tested for differences among and within sites. Males had shallower rostrum, increased head width and length, decreased abdomen and cephalothorax width and length, and increased telson length compared to females. Morphology of males did not vary with stream or along an urban gradient. The morphology of females varied with stream and along an urban gradient. Female shapes from small creek sites were stouter and less fusiform than larger river specimens. Following an urban gradient, females exhibited an increasingly reduced abdominal and telson area and a more fusiform rostrum. Morphological variation is linked with adaptation and subsequent success of aquatic taxa. Disentangling the potential influences on crayfish morphology has implications for improved understanding of ecosystem structure and conservation.