Despite identification of multiple factors mediating salmon survival, significant disparities in survival-to-adulthood among hatchery- versus wild-origin juveniles persist. In the present report, we explore the hypothesis that hatchery-reared juveniles might exhibit morphological defects in vulnerable mechanosensory systems prior to release from the hatchery, potentiating reduced survival after release. Juvenile steelhead (Oncorhynchus mykiss) from two different hatcheries were compared to wild-origin juveniles on several morphological traits including lateral line structure, otolith composition (a proxy for auditory function), and brain weight. Wild juveniles were found to possess significantly more superficial lateral line neuromasts than hatchery-reared juveniles, although the number of hair cells within individual neuromasts was not significantly different across groups. Wild juveniles were also found to possess primarily normal, aragonite-containing otoliths, while hatchery reared juveniles possessed a high proportion of crystallized (vaterite) otoliths. Finally, wild juveniles were found to have significantly larger brains than hatchery-reared juveniles. These differences together predict reduced sensitivity to biologically important hydrodynamic and acoustic signals from natural biotic (predator, prey, conspecific) and abiotic (turbulent flow, current) sources among hatchery-reared steelhead, in turn predicting reduced survival fitness after release. Physiological and behavioral studies are required to establish the functional significance of these morphological differences.