In the last decade the United States has witnessed hundreds of dam removals motivated by ecological, economic and safety concerns. Multiple countries including Japan, Australia, and France have either removed or are planning to remove dams to restore native ecosystems. Despite the potential for dam removal to restore freshwaters, few dam decommissionings have accompanying research programs to evaluate the ecological costs and benefits of dam removal. The handful of published studies on dam removal yield mixed results. Here we present the responses of native fish and macroinvertebrates to flow restoration and the removal of exotic fish associated with the decommissioning of a large hydropower dam in Fossil Creek, Arizona. Stable isotope analysis and fish surveys conducted prior to restoration indicated that native fish were limited more by the presence of exotic fish than reduced flow. Fish surveys conducted a year after restoration support this prediction indicating that native fish increased significantly only where exotic fish were removed. In contrast, native fish populations showed modest increases where flow was restored, increases that were not significantly different from control sites. Macroinvertebrate communities changed substantially after restoration. In some sites macroinvertebrate communities now resemble upstream control sites whereas in other sites new communities are emerging.