Trait-based models of ecological communities and ecosystem functioning often fail to account for intraspecific variation in functional traits, assuming that intraspecific variability is negligible compared with interspecific variability. However, this assumption remains poorly tested across vertebrate animals where past studies routinely describe species according to mean trait values without explicit consideration of individual trait variability. We assessed nine functional traits for 4254 individuals belonging to 15 freshwater fish species from 11 families in northern Australia, including body elongation, body shape, caudal peduncle throttle, eye size, eye position, gape shape, gape size, mouth position, and pectoral fin length. We quantified the extent and geography of intraspecific trait variability and its relationship with riverine hydrologic regimes using a structured sampling design. Using a combination of single- and multi-trait analyses, we demonstrate that intraspecific trait variability can contribute up to 70% of the total trait variability depending on the attribute considered and averaged 31% across all traits. The magnitude of intraspecific trait variability also varied across the hydrological permanency gradient. Fish assemblages in intermittent streams subjected to frequent environmental disturbance had high intraspecific trait variability, most likely due to strong abiotic filters limiting interspecific divergence. Conversely, assemblages in perennial rivers with less harsh environmental filters but with a larger pool of species expressed lower intraspecific trait variability: This is most likely due to stronger resource competition (biotic filter), which promotes specialization of resource use and, consequently, interspecific divergence. Our study provides the first evidence of intraspecific trait variability driven by a disturbance gradient for an animal group and points to the need for additional research into the functional importance of intraspecific variability in animal ecology. A better understanding of the patterns, drivers, and implications of intraspecific trait variability will help guide mechanistic-based predictions of the effects of environmental changes on community assemblage and ecosystem processes.