Intraspecific variability, although comparably less studied than interspecific variation, is an important tool in understanding population responses to environmental gradients. This study investigated intraspecific trait variation across three contrasting aquatic flow habitat types (intermittent creek, billabong and river) in a common mouth-brooding freshwater fish in northern Australia, the mouth almighty Glossamia aprion. Samples of G. aprion were collected at various sites, within the Daly River catchment. It was predicted that a number of morphological and reproductive traits would vary among individuals across the contrasting habitats. Five out of the nine morphological and reproductive traits studied significantly varied across flow habitat types. Significant intraspecific variation in functional traits related to foraging and reproduction, such as relative eye size, eye vertical position and relative maxillary length in males suggest that the inherent characteristics of each flow habitat type could be exerting selective pressure on the morphology of G. aprion. Interestingly, traits related to swimming performance (body lateral shape) and manoeuvrability (pectoral fin ventral position) differed between flow habitat types but showed inconsistent responses to predictions. Whilst this study was temporally and spatially limited, it highlights that intraspecific variability in morphological traits can occur among flow habitat types over relatively small spatial scales.