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 regards to spawning. We evaluated the relationship between morphology and habitat measures, such as current velocity, slope, and substrate particle size, in spawning Robust Redhorse (n = 58) and Notchlip Redhorse (n = 43) from the lower Savannah River, South Carolina-Georgia. Individuals of both species were captured using prepositioned grid electrofishers deployed, measured, and photographed before being released. We constructed a truss network and 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 variable for Robust Redhorse. Robust Redhorse captured from the deeper locations with higher current velocities had lower aspect ratio heads than those of 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.