We compared body morphology of two freshwater sculpin taxa that inhabit distinct environmental conditions in the Chesapeake Bay watershed of eastern North America: Potomac sculpin (C. girardi, Robins; PS) and checkered sculpin (C. sp. cf. girardi; CS). Both taxa are endemic to the study area, but PS are more broadly distributed than CS which are limited to karst groundwater-dominated streams in the central Potomac River basin. We examined preserved specimens from sites encompassing their geographic range (six sites per taxon) to evaluate taxonomic differences and environmental effects. Pelvic fin ray counts and body shape distinguished the study taxa. Morphological variation exhibited stronger relationships to environmental covariates (site elevation and basin size) in PS than CS as expected. In addition, the frequency of specimens with a united median chin pore increased with site elevation in PS (but not CS), suggesting thermal effects on preoperculomanibular canal development. However, contrary to expectation, PS did not exhibit greater among-population variation in body shape than CS, and this indicates the potential importance of unmeasured environmental differences among karst groundwater-dominated streams in the study area. Our study also indicated the utility of stream-level management units for CS, an undescribed species recognized as “critically imperiled” by state agencies.