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INTRODUCTION Conservation and management of native species is now a major consideration within the Colorado Division of Wildlife (CDOW). This is especially true for species that are listed as federally threaten or endangered. Four species offish in the Colorado River basin are listed as endangered by the U.S. Fish and Wildlife Service. The Upper Colorado River Recovery Program was established to identify and resolve problems, so these fish can eventually be down-listed (Wydoski and Hamill 1991). The state of Colorado and the Recovery Program share the same goal of recovering the fish, but their agencies may not share common strategies. A unifying approach for native fish management objectives is to agree on the scientific validity of data involved in identification of limiting factors. In Colorado State government instream flow protection for fish via water rights has been a common practice in high elevation headwaters (Espregren 1998). Water rights adjudication, however, has become a rigorous legal process for high profile warm water rivers like the Colorado and Yampa Rivers where water is already highly over- appropriated. In response, U. S. Fish and Wildlife Service (LJSFWS) conducted studies for instream flow recommendations in regard to recovery of endangered fish species in the 15-Mile Reach of the Colorado River (Osmundson et al. 1995) and the Yampa River (Modde and Smith 1995). Modde et al. (1999) was afield-based study on the Yampa River, also sponsored by the Recovery Program. Even though the intent of these flow studies was the same, to determine stream flow requirements for endangered fish, recommendations were based on vastly different methodologies. The goal of this project was to develop biologically based instream flow recommendations for the Colorado in the 15-Mile Reach and Yampa rivers based on habitat and flow requirements for non-endangered native fish. The identification and validation of flow needs for non-endangered native fish may assist in preventing listing these species in the future. This data may also be of value to the Endangered Fish Recovery Program by providing ancillary information concerning the overall fish community and descriptions of physical habitat availability. Typically CDOW uses the R2Cross method (Nehring 1979) or PHABSIM (Bovee 1982) for making instream flow recommendations for protecting cold water habitats. However these two methods were not considered appropriate for the warm water sections of the Colorado and Yampa Rivers given the elevated levels of biological, geomorphic and social complexities for these rivers. This study employed a Meso-Habitat approach that is similar in concept to PHABSIM. PHABSIM is widely used in North America to quantify impacts of altered flow regimes to habitat. PHABSIM consists of two modeling components. The hydraulic component is a series ofone-dimensional cross-sections that are linked to produce a series of rectangular cells that form a grid. Mean depth and velocity conditions are calculated for each cell for a given flow. The biological component is a set of suitability index curves for depth and velocity criteria that are used to rate micro-habitat suitability for each cell in the cross-sectional grid. Habitat availability is measured by an 12