The endangered bonytail Gila elegans, a large-bodied, main-stem cyprinid endemic to the Colorado River Basin of the American Southwest, was once widespread and abundant in warm-water-stream reaches. Negative effects of altered flow and temperature regimes downstream of dams, other habitat changes, and establishment of nonnative fishes have reduced populations of native fish throughout the basin, and wild bonytails may be extirpated. Hatchery reared bonytails are stocked in formerly occupied habitat to rebuild depleted populations, but their ecology is poorly understood. In 2002–2007, sampling in the middle Green River from upstream and downstream of stocking locations in Dinosaur National Monument documented survival of bonytails for ≤4 months, but apparently none survived longer. Many fish at large ≤4 months had Lernea or fungal infections, weighed an average of 20% less than fish when released, and had relatively low rates of growth. Post-stocking rates of dispersal downstream (ca. 1 river km/day) were considerable, and potentially, biologically significant. Bonytails occupied pools, eddies, runs, backwaters, and riffles, and co-occurred in eddies with the roundtail chub Gila robusta and humpback chub Gila cypha in Whirlpool Canyon. We also documented two instances of predation by smallmouth bass Micropterus dolomieu on bonytails ≤225 mm in total length. Reduced predation by large-bodied, nonnative, piscivores and increased resistance to disease and other stressors that reduce body condition may increase survival of stocked bonytails in this portion of the Green River. Alternative stocking strategies, including use of alluvial and floodplain areas, and effects of size on survival, are being evaluated.