The biomass of organisms of different sizes is increasingly being used to explore macroscale variation in food-web and community structure. Here we examine how invasive species and river flow regulation affect native fish biomass and fish community log10 biomass – body mass scaling relationships in Australia’s largest river system, the Murray–Darling. The log10 biomass – body mass scaling exponent (scaling B) of invasive fishes (95% CI: −0.14 to −0.18) was less negative than for native fishes (95% CI: −0.20 to −0.25), meaning that invasive species attained a higher biomass in larger size-classes compared to native species. Flow alteration and invasive common carp (Cyprinus carpio) biomass were correlated with severe reductions in native fish biomass ranging from −47% to −68% (95% CI). Our study provides novel evidence suggesting that invasive and native communities have different biomass – body mass scaling patterns, which likely depend on differences in their trophic ecology and body size distributions. Our results suggest that restoration efforts using environmental flows and common carp control has potential to boost native fish biomass to more than double the current level.