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INTRODUCTION The endangered humpback chub (Gila cypha) only lives in those canyon reaches of the Colorado River system where there are abundant debris fans and rapids, such as Desolation and Gray Canyons of the Green River in eastern Utah. In addition to humpback chub, Desolation and Gray Canyons support populations of the endangered Colorado pikeminnow (Prychocheilus Lucius), and contain one of the few known spawning sites of this species. Because the operation of Flaming Gorge Dam has the potential to affect the habitats of these endangered fish, we investigated the relationship between discharge, habitat availability, and habitat distribution in Desolation and Gray Canyons. Habitat characteristics are determined by flow and substrate conditions. Gravel bars are abundant in these canyons, and much of the banks are composed of coarse debris flow material or talus. However, other banks are composed of sand, silt, and clay deposited as suspended load. Recirculating eddies comprise a large part of the flow field of the river, and there are many regions of upstream or stagnant flow in these canyons. Preferred habitat at different life stages of the humpback chub occur as various combinations of channel substrate, bank material, and local hydraulics. The most comprehensive studies of habitat for these fish at various life stages have been conducted on the Colorado River and the Little Colorado River in Grand Canyon, where the Colorado River's sediment load, temperature, and discharge differ substantially from the relatively unregulated conditions of the Green River. Valdez and Ryel (1995) showed that adult humpback chub spend most of their lives in low-velocity parts of large, recirculating eddies. Converse (1996) found that juvenile humpback chub in Grand Canyon prefer small eddies and low-velocity zones along vegetated shorelines and along some bedrock banks that have overhanging cliffs. In Desolation and Gray Canyons, preliminary findings by Day and Crosby (1997) show that humpback chub, on average, use eddy habitats that were longer, and wider than unused eddies. However, habitat preferences are still not well understood in these canyons. .Thus, we identified various combinations of flow and substrate that have the potential to constitute important habitat. Our purpose was to determine if the size and abundance of these habitats changes with discharge. Local flow patterns and type of substrate are influenced by seasonal and dam-related changes in discharge. Schmidt (1990) showed that recirculating eddies increase in length with increasing discharge. As discharge increases, shorelines, vegetation, and mid-channel bars are inundated, and the amount of shoreline within eddies changes. Thus, the distribution of desirable habitat may change. Releases from Flaming Gorge Dam influence base-flow of the Green River in Desolation/Gray Canyons as well as the timing and magnitude of spring floods. Significant changes in the geomorphology of the Green River have taken place during the past century which have the potential to alter the relationship between discharge and habitat. Increases in riparian vegetation, channel narrowing, abandonment of secondary channels, and the subsequent loss of habitat have been well documented in reaches upstream and downstream from Desolation and Gray Canyons (Graf 1978, Allred 1997, Grams 1997). Allred (1997) showed that channel narrowing and simplification near Green River, Utah, occurred during 2 periods.' The first period was during the regional drought of the 1930s, and the second period followed the completion of Flaming Gorge Dam. Although the introduction of the nonnative tamarisk (Tamarix sp.) helped cause narrowing, the primary mechanism was reduced flood magnitudes due to climate change and flow regulation. Because no studies have measured the extent of A-1