Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis, remains a health threat to salmonid fish in the western United States. Although various aspects of this host–parasite system have been studied, investigations examining the overall epizootiology of whirling disease in an ecosystem are lacking. Therefore, in June 1998, studies were initiated in the Rock Creek watershed of west-central Montana and continued through 2003 to assess the intensity of infection in trout using sentinel cages stationed throughout the drainage. Additional studies determined the percentage of the annelid worm, Tubifex tubifex, releasing M. cerebralis at various localities in Rock Creek and whether there was a seasonal or daily periodicity in the release of the triactinomyxon stage of the parasite from T. tubifex. Lastly, habitat and water quality parameters, and the effects of habitat restoration on transmission of M. cerebralis, were assessed. Overall, the intensity of M. cerebralis infections in sentinel trout increased significantly throughout the drainage between June of 1998 and 2003, with the biggest jump occurring between 1998 and 1999. In addition, the range of M. cerebralis expanded considerably over the period of study. There was no strict correlation between habitat condition and the occurrence of the parasite; fish became heavily infected in optimal and marginal habitats. However, fish exposed at a locality that had the lowest habitat ranking consistently had the highest intensity of infection. The parasite has apparently caused a dramatic decline in rainbow trout densities, but the brown trout population numbers have increased, and the overall fish density remains high. Although a major habitat restoration project did not seem to have an effect on decreasing disease intensity, this was not surprising because the restored area was located just downstream from a “hotspot” of infected T. tubifex.