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Lahontan cutthroat trout, Oncorhynchus clarki henshawi, are currently limited in their distribution to a patchwork of small isolated populations, the result of habitat degradation and natural variation in landscape and in-stream conditions. The objectives of this study were to determine if landscape topography influences trout distribution, and if water temperatures control this response. The work was carried out in a sub-basin of the Quinn River system, McDermitt Creek, which drains the sagebrush desert of southeastern Oregon and northern Nevada. Head-water tributaries of this creek consist of alternating canyon-confined and valley bounded reaches. Trout within these systems are challenged by low discharge and high temperatures during the summer, and anchor ice during the winter. Contiguous whole stream surveys were used to look at trout distribution during the summer of 2003 and spring and fall of 2004. Our results suggested that topography can affect trout distribution. Trout numbers were highest in areas with greater numbers of nick-points (the transition zones between less confined and more confined valley segments) and greater valley confinement. Additionally, in the downstream portion of our headwater reaches, more trout were found in nickpoints than expected based on the availability of this habitat type. Our data suggest that hyporheic inputs may be high in such areas, thus providing trout with shelter from warm water in the summer, anchor ice in the winter, and shallow stream depths during all seasons. Spatial occurrence of these areas of refugia can be taken into consideration when planning land use activities and restoration efforts. Further research is required to confirm that topography can affect the distribution of Lahontan cutthroat trout in other systems, and to better understand the mechanisms behind these patterns.