Research has been conducted on defining what physical habitat, i.e., habitat suitability criteria (HSC), is suitable for various Arizona fishes; however, most of this work has focused on the relationship of fish presence with flow, depth, and substrate habitat. Less is known about the relationship of other factors, such as overhead cover, instream cover, riparian vegetation, channel morphology, and water temperature to desert fish species presence. Furthermore, fish habitat use can vary among streams. It has long been known that fish can partition themselves in different habitats, depending on other species present. Therefore, examining how preferred habitat varies with the presence of other species gives a clearer answer as to how fish distribution is shaped under a variety of conditions. Fossil Creek is a tributary of the Verde River Fossil Creek that supports five species of native fishes and represents a unique type of habitat for these organisms. It has a barrier between fish habitat that contains only native species and that which contains both native and nonnative species, allowing for comparison of habitat use. The stream is a travertine system, highly charged with calcium carbonate and dissolved CO2. The goal of this project was to identify specific physical and biological habitat needs of select fish species in Fossil Creek that will allow for improved habitat management, provide information to aid in protection of in-stream flows, and contribute to recovery of endangered and sensitive native fish species. Fossil Creek also provided us with the opportunity to examine native fish habitat use in the presence and absence of nonnative species. This information is being combined with that from a co-occurring project on habitat suitability criteria being conducted across the Verde and several other Arizona rivers and streams in the development of river specific and generalized habitat suitability criteria. To date we have conducted fieldwork in Fossil Creek and analyzed data. Results are being prepared for publication.