The presence of nonnative trout and the recent introduction of Myxobolus cerebralis in the Logan River drainage pose a threat to the native Bonneville cutthroat trout population (Oncorhynchus clarki Utah). The variability in the response of susceptible trout populations to M. cerebralis, causing agent of whirling disease, suggests that environmental factors may influence the effects of the parasite in infected environments. I investigated the relationship between temperature, discharge, substrate size, nutrient concentration (nitrogen and phosphorus), periphyton (chlorophyll a), and the relative abundance of Tubifex tubifex to the distribution, and prevalence of M. cerebralis in wild salmonid populations and sentinel fish in the mainstem of the Logan River and two of its tributaries. In addition, I investigated the potential influence of biotic (e.g., food availability, M. cerebralis prevalence) and abiotic factors (e.g., temperature) on the distribution abundance, and condition of salmonid fishes. Differences in mean temperature and discharge across sites explained most (>70%) of the variability in prevalence of M. cerebralis observed along the Logan River. However, the prevalence of the parasite was not related to other factors that can influence its life cycle, such as productivity and substrate composition. The results also indicate that the fish fauna presents a longitudinal change reflected in a zonation pattern. Cutthroat trout dominates the headwaters and high-elevation reaches, while reaches at lower elevations of the mainstem and tributaries were dominated by brown trout. The transition between these species was consistent with changes in environmental characteristics. Cutthroat trout dominates the fish community in mainstream reaches with the lowest average minimum temperature and highest diel temperatures, and where small boulders and small cobbles are the predominant substrate. This study provides insights of the abiotic and biotic factors that affect the distribution, abundance, and condition of salmonid populations along the Logan River. Identifying these factors is crucial to effectively manage this and other trout streams, where ensuring the conservation of native cutthroat trout populations is a priority. Further, I present baseline information of the potential linkages between environmental factors and M. cerebralis distribution and prevelance, which could be used to develop plans to minimize the potential negative effects of this parasite on wild salmonid populations.