Tributaries of the Colorado River Basin, historically home to a complex of endemic omnivores collectively referred to as the ‘three species’; flannelmouth sucker (Catostomus latipinnis), bluehead sucker (C. discobolus) and roundtail chub (Gila robusta), have experienced the establishment of numerous non-native fish species. In this study, we examine the impacts of the trophic ecology of non-native fishes on the ‘three species’ in the San Rafael River, Utah, USA. We employ a suite of abundance comparisons, stable isotope techniques and size-at-age back-calculation analyses to compare food web structure and growth rates of the ‘three species’ in study areas with and without established populations of non-native species. We found that the ‘three species’ are more abundant in areas with few non-native fishes present, regardless of habitat complexity. Stable isotope analyses indicate non-native fishes lengthen the food chain by 0.5 trophic positions...