Maintaining intraspecific diversity is an important goal for fisheries conservation and recovery actions. While ecomorphological studies have demonstrated intraspecific diversity related to feeding or flow regime, there has been little assessment of such variation in regard to spawning habitat. We evaluated the relationship between individual morphology of Robust Redhorse and Notchlip Redhorse and variables describing the spawning habitat from which they were captured, such as current velocity, depth, and substrate particle size. Robust Redhorse (n = 58) and Notchlip Redhorse (n = 43) were captured from spawning aggregations in the lower Savannah River, South Carolina-Georgia using prepositioned grid electrofishers. They were then measured and photographed before being released. We constructed a truss network using digitized landmarks on each of the photographs. Relationships between the morphological and environmental datasets were assessed using canonical correlation analysis. In both species, these morphological predictors were correlated primarily to depth, though current velocity also contributed to the environmental canonical score for Robust Redhorse. Robust Redhorse captured from the deeper locations with higher current velocities had heads with lower aspect ratio compared to individuals captured from shallower areas. Notchlip Redhorse from shallower areas were deeper-bodied and had shorter trunks than counterparts from deeper areas. These differences suggest that ensuring spawning habitat heterogeneity may be an important component to conserving intraspecific diversity, particularly in systems where such habitat is limiting.