Nursery habitat availability is considered a bottleneck to successful recruitment of Colorado squawfish (Ptychocheilus Lucius). Detailed geomorphic studies were conducted in a 1.5-km reach to examine channel response to flows and the geomorphic setting of nursery habitats during a 2-year period. Videography was used to extend relationships in the 1.5-km reach to a longer 10-km reach. Nursery habitat availability varied yearly with little persistence in location or geomorphic setting of individual habitats for the 2 years of this study. A small number of habitats provided most of the area of high-quality (i.e., deep) habitat, and most of the total area of habitat was formed by three geomorphic classes. Although the 1993 flood reduced the area of available habitat, area of deep habitat increased. The 1994 low-peak flood increased the area of habitat, but most habitats were shallow. The 1993 and 1994 multi-peaked habitat availability curves for the 1.5-km-reach bank-attached bar were the result of the superposition of curves from habitats in each geomorphic classification, and showed that the discharge that maximized habitat availability changed yearly. A complexity index was evaluated for the 10-km reach as surrogate for habitat availability. Total base-flow habitat availability was significantly correlated to the complexity index, but deep habitat availability was not. Measured channel topography was used as input to a flow and sediment transport model. Simulated hydrograph runs produced greater bank-attached bar aggradation and thalweg scour than steady flows, although some unrealistic patterns of scour occurred. New flow recommendations must include occasional high flows sufficient to rebuild channel topography. Flaming Gorge Dam releases should be used to augment the Yampa River flood peak, but not increase low flood-peak duration. The conceptual model for habitat availability developed here may be used to target the formation and availability of habitats. Base flow recommendations designed to maximize habitat availability should be evaluated annually. Winter flows should be reevaluated for their negative effects on habitat.