The highly endemic native fish fauna has experienced dramatic reductions in abundance and range because of anthropogenic activity. In addition to a highly altered flow, temperature, and physical habitat template, many non-native fish species have established populations throughout the basin. The San Rafael River, a tributary of the Green River in southeastern Utah, is home to populations of flannelmouth sucker (Catostomus latipinnis), bluehead sucker (C. discobolus), and roundtail chub (Gila robusta), and has experienced degradations representative of many rivers throughout the Colorado River Basin. Using the San Rafael River as a template, I examined (1) the effect of the non-native fishes on the food web structure of a Colorado River tributary and (2) whether any changes to the food web structure by non-native fishes impact fitness-related vital rates of native fishes in the river. Stable isotope analysis revealed that the non-native fishes present novel predator archetypes to the “three species,” but size-at-age and body condition analyses did not reveal any reduction in fitness between native fishes captured in the presence of the non-native fishes. Additionally, I used site-specific biotic and abiotic measurements to develop a model predicting “three species” relative abundance. Non-native fish abundance and spatially auto-correlated measures of physical habitat were found to be particularly important predictors of “three species” relative abundance. The model was used in combination with a longitudinal habitat survey to predict the current continuous distribution along the length of the lower San Rafael River, as well as to simulate population-level effects of relevant restoration actions. The eradication of non-native fishes resulted in significant population increases for each of the ‘three species,’ and physical habitat restoration resulted in significant population increases when executed in certain reaches, but significant population reductions if executed in other reaches. These results suggest that the restoration of physical habitat without addressing populations of non-native fishes will likely result in a limited response by the “three species,” and that the choice of restoration location is critical to its success.