The western rainbowfish, Melanotaenia australis, is abundant and widespread across streams of the Pilbara region of northwest Australia. Hydrological flow regimes are highly dynamic and can vary from no flow to rapidly flowing depending on the landscape and season. However, little is known of the plasticity and resilience of M. australis to spatial variation in habitat conditions. We measured morphological variation in M. australis across 11 sites along a 450 km section of the Fortescue River in the Pilbara. We sought to (i) quantify body shape variation across the catchment using landmark-based geometric morphometric analyses, and (ii) assess if morphological variation corresponded to habitat conditions (water velocity, pool size and chemistry, catchment position, predation and diet). We found that M. australis exhibits a range of morphologies, with differing body depths explaining the most variation in shape (45.97%). Preliminary analysis indicates that the morphology of M. australis differs according to sex and catchment region of the Fortescue River. Flow rates and habitat complexity, which are commonly reported to affect body shape in other fish species, did not explain morphological variation of M. australis across our study sites. However, flow rates within the catchment were low (all less than 1 m/sec); on-going work is assessing how M. australis may alter body shape at higher flows.