Anthropogenic habitat alteration creates novel environments that can alter selection pressures. Construction of reservoirs worldwide has disturbed riverine ecosystems by altering biotic and abiotic environments of impounded streams. Changes to fish communities in impoundments are well documented, but effects of those changes on native species persisting in reservoirs, which are presumably subjected to novel selective pressures, are largely unexplored. I assessed body shape variation of a native stream fish in reservoir habitats and streams from seven reservoir basins in the Central Plains of the USA. Body shape significantly and consistently diverged in reservoirs compared with stream habitats within reservoir basins; individuals from reservoir populations were deeper-bodied and had smaller heads compared with stream populations. Individuals from reservoir habitats also exhibited lower overall shape variation compared with stream individuals. I assessed the contribution of genotypic divergence and predator-induced phenotypic plasticity on body shape variation by rearing offspring from a reservoir and a stream population with or without a piscivorous fish. Significant population-level differences in body shape persisted in offspring, and both populations demonstrated similar predator-induced phenotypic plasticity. My results suggest that, although components of body shape are plastic, anthropogenic habitat modification may drive trait divergence in native fish populations in reservoir-altered habitats.