We applied the index of biotic integrity (IBI) to the portion of the Arkansas River basin within the Southwestern Tablelands ecoregion, located on the Great Plains of southeastern Colorado. Only nine IBI metrics were appropriate for this region, largely because of the depauperate and tolerant ichthyofauna. The modified index was then used to assess effects of U.S. Army mechanized infantry training on biotic integrity of the Purgatoire River at 12 sites adjacent to the Pifion Canyon Maneuvers Site, a remote and relatively undisturbed canyon reach on a seventh-order Arkansas River tributary. Decrease in abundance of adult red shinersCyprinella lutrensis, a tolerant omnivorous species, over a 6-year period (1983–1989) caused marked increases in the IBI at 9 of 12 sites despite lack of obvious changes in environmental quality after training began in 1985. Neither sampling variation nor the magnitude and timing of floods were sufficient to explain the large decrease in red shiner abundance. Other attributes of the biota, such as presence of long-lived fishes and lack of introduced species, provided no evidence for detrimental change. The majority of potential IBI metrics were hampered by the low fish species richness, the preponderance of trophic and habitat generalists, or other attributes of the depauperate ichthyofauna. Moreover, human perturbations that cause change in fish communities of midwestern U.S. streams are suspected in many cases to mimic natural disturbances in this system, so they may have relatively little effect. Conversely, some perturbations considered benign in more mesic environments are likely to cause dramatic changes. We therefore propose that our understanding of the structure, function, and natural variation of fish communities in western Great Plains streams must increase substantially before we can define fully appropriate measures of biotic integrity for these lotic systems.