Quantifying variation in functional traits across a range of taxonomic and environmental scales can provide insight into species’ niche requirements and mechanisms of community assembly, and be used to predict ecological responses to changing environmental conditions. This paper synthesises our recent work to understand the environmental, spatial and phylogenetic determinants of freshwater fish life-history traits and functional composition of Australian rivers. We also examine the phylogenetic and spatial structure of intra-specific variation in key life-history traits of the Australian smelt Retropinna semoni sampled across a gradient of hydrologic variability in 19 eastern Australian rivers. Variation in total fecundity had a stronger phylogenetic signal than variation in egg size. After accounting for the influence of phylogeny, spatial variation in both life history traits was related to gradients of hydrologic predictability and stability. Intra-specific variation in fecundity and egg size, coupled with low spatial autocorrelation at scales of population connectivity up to 100 km, and differences in life-history trait expression between geographically distinct clades observed in this study, suggest a high potential for ambiguous trait-environment relationships in studies conducted at coarse spatial grains (e.g. river basins) or higher taxonomic levels (i.e. species). Quantifying the spatial structure of intra-specific life-history trait variation, key intra-specific trait-environment relationships, and the rates at which life-history traits may respond to local conditions within a phylogenetic framework in this study has important implications for future works seeking to understand population or species responses to changing environmental conditions at local to regional scales.