The riparian habitats of the arid southwestern United States provide critical stopover habitat for avian migrants, but they have been severely altered by invasive tamarisk (Tamarix spp.). The responses of birds to such habitat alterations are not well understood. We combined ecological and physiological measurements to provide an integrative assessment of how tamarisk invasion affects the stopover ecology of vernally migrating Wilson's Warblers (Wilsonia pusilla) along the San Pedro River in Arizona. Despite higher arthropod biomass in native cottonwood—willow habitat, the refueling rate of Wilson's Warblers, as measured by plasma metabolite profiling, was higher in tamarisk. Density and detections of Wilson's Warblers did not differ between habitats, but both measurements were significantly higher in cottonwood—willow habitat for the other members of the Wilson's Warbler foraging guild. Our measurements of food resources and migrant densities suggest that cottonwood—willow may provide high-quality stopover habitat. But when plasma metabolites are included, our results indicate that tamarisk offers superior habitat for refueling Wilson's Warblers, possibly because of release from high interspecific competition in cottonwood—willow. Our results demonstrate the importance of measuring refueling performance in the assessment of stopover habitat quality and the value of including plasma metabolite profiling in studies of avian stopover ecology.