Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis, is a serious health threat to salmonid fish and its control remains problematic. The parasite has a 2-host life cycle involving a salmonid and the aquatic oligochaete Tubifex tubifex. A commonly used strategy to control parasites that requires an obligatory invertebrate host is to eliminate or reduce the host population size to a point where parasite transmission can no longer occur. Large numbers of T. tubifex are frequently found in degraded habitats that are characterized by an abundance of fine sediments, organic matter, and a lack of aquatic invertebrate diversity. If such environments are rehabilitated, then the normal flora and fauna should re-establish and the numbers of T. tubifex should decline due to their inability to compete with the re-established invertebrates. During an epizootiological study on Rock Creek, located in west-central Montana, 2 opportunities were available to examine the effects of habitat restoration on the transmission of M. cerebralis. The Puyear Ranch re-establishment project was a major endeavor conducted on the main channel of Rock Creek, a little more than midway upstream. Another significant restoration was conducted on Upper Willow Creek, a tributary of Rock Creek, located closer to the headwaters. Sentinel trout studies, along with examining T. tubifex for the parasite and measuring various water-quality parameters, revealed that the restoration of the Puyear Ranch locality had no significant effect on reducing the intensity of M. cerebralis in trout. This was likely due to the restored area being located mid-river, just downstream from a “hot spot” of infected T. tubifex. In comparison, there was a significant reduction in the intensity of M. cerebralis in sentinel fish after the Upper Willow Creek restoration project was completed. Unlike the Puyear Ranch locality, there was no hot spot of infected T. tubifex above the area rehabilitated on Upper Willow Creek. Further, the relative abundance of T. tubifex and M. cerebralis-infected worms was reduced. Although further study is needed, it appears that habitat rehabilitation can reduce the transmission of M. cerebralis. Since the triactinomyxon stage of the parasite released from T. tubifex (which infects trout) can float for many kilometers, the rehabilitation of a hot spot may reduce the infection of trout downstream where they inhabit a healthy environment with no M. cerebralis-infected T. tubifex in the vicinity. Thus, rehabilitation of a relatively small area could significantly affect the drainage for many kilometers beyond the improved habitat.