Glen Canyon Dam has greatly altered the Colorado River in Grand Canyon. The Little Colorado River (LCR) provides a small refuge of seasonally warm and turbid water that is thought to be more suitable than the Colorado River for endangered humpback chub Gila cypha. However, the LCR has low productivity and contains nonnative fishes and parasites, which pose a threat to humpback chub. The Colorado River hosts a different suite of nonnative fishes and is cold and clear but more productive. We compared condition factor (K), abdominal fat index (AFI), and presence and number of two introduced pathogenic parasites (Lernaea cyprinacea and Bothriocephalus acheilognathi) between juvenile (<150 mm total length) humpback chub from the LCR and those from the Colorado River during 1996a??1999. Both K and AFI were lower and L. cyprinacea prevalence and B. acheilognathi prevalence were higher in LCR fish than in Colorado River fish for all years. Mean K and AFI were 0.622 and 0.48, respectively, in the LCR and 0.735 and 2.02, respectively, in the Colorado River, indicating that fish in the Colorado River were more robust. Mean prevalence of L. cyprinacea was 23.9% and mean intensity was 1.73 L. cyprinacea/infected fish in the LCR, whereas prevalence was 3.2% and intensity was 1.0 L. cyprinacea/infected fish in the Colorado River. Mean prevalence of B. acheilognathi was 51.0% and mean intensity was 25.0 B. acheilognathi/infected fish in the LCR, whereas prevalence was 15.8% and intensity was 12.0 B. acheilognathi/infected fish in the Colorado River. Increased parasitism and poorer body condition in humpback chub from the LCR challenge the paradigm that warmer LCR waters are more suitable for humpback chub than the colder Colorado River and indicate the need to consider the importance and benefits of all available habitats, as well as biotic and abiotic factors, when managing endangered species and their environment.