Significant differences in growth and prespawning body morphology were detected among three stocks of Atlantic salmon reared in a common marine environment. Smolts originating from river-specific broodstock of the Machias, East Machias, and Dennys populations were reared at two marine net-pen facilities for 25 months. Significant differences in stock-specific growth were observed among two stocks at both sites, suggesting a genetic basis for the observed phenotypic variation. There was a significant stock effect to the total measured phenotypic variation based on collected truss network analyses. Linear discriminant function analysis of a truss network of morphometric distances allowed for 73% accuracy of stock classification. A thin-plate spline procedure characterized the Machias body form as having a shortened narrow caudal peduncle region, a compressed body with an elongated trunk, and a deeper head region relative to the other two stocks. Phenotypic variation may be associated with hydrological characteristics of the Machias watershed.