We evaluated the potential of habitat restoration to improve stream and riparian habitat and to minimize the prevalence of whirling disease in a population of native cutthroat trout in northern Utah. We fenced 67 ha of riparian habitat to exclude livestock and measured key response variables at impact and control sites before and after the completion of the exclosure. Total N concentrations decreased in response to the exclusion. Over this short time period (1–2 y postrestoration), the combination of natural variability and exclusion of livestock grazing appeared to alter the vegetation and riparian conditions through increased bank stability and decreased % cover of exotic plant species. The effect of the exclosure on whirling disease was confounded by climatic variation. However, restoration appeared to reduce the prevalence of whirling disease during a nondrought year, but not during a drought year. Therefore, in the short term, these beneficial effects of restoration on trout appeared to hinge on favorable climatic conditions. We expect the longer-term restoration response to be affected less than the short-term response by climatic conditions. The results of our study indicate that passive stream restoration is an effective management approach for restoring stream habitat and has the potential to minimize interactive effects of disease and habitat degradation, especially when other options for disease management are not possible or practical.