Landmark‐based geometric morphometrics were used to evaluate the effect of flow and depth in the water column on the body size and shape of Brycon henni from river and stream populations. The dendrogram showed that stream populations clustered apart and showed significantly smaller centroid size and narrower bodies than river populations, indicating a role for flow and depth on whole body morphometric variation. The results are concordant with morphometric variation described in other fish species and provide the first insights into phenotypic variation in natural populations of B. henni.