The effects on trout of the whirling disease parasite Myxobolus cerebralis were evaluated to observe whether they could be ameliorated by intervening with physical habitat manipulations. Physical stream habitat was modified at field sites in Spring Creek and Williams Fork River, Colorado, USA to reduce or eliminate habitat for the invertebrate oligochaete host of M. cerebralis, Tubifex tubifex. Data were collected before and after habitat modifications on total oligochaete and T. tubifex biomass, actinospore production from oligochaete samples, surface water actinospore concentrations, and prevalence and intensity of myxospore development in Brown Trout, Salmo trutta. Oligochaete biomass estimates lacked precision due to inherently patchy distribution of the target organisms. Oligochaetes quickly re-occupied a portion of habitat at the Williams Fork River site, but oligochaete biomass was depressed for nearly a year at the Spring Creek site. All T. tubifex in Spring Creek belonged to a susceptible lineage, but in the Williams Fork River there was a mix of susceptible and non-susceptible T. tubifex. Actinospore detection in filtered surface water samples showed consistent but minor reduction in density in Williams Fork River and no difference or even higher densities in Spring Creek after habitat modification. Myxospore prevalence and intensity of infection in Brown Trout appeared to decrease in Williams Fork River after habitat modification, but there is evidence that a similar decrease also occurred at a control site in that stream. Spring Creek showed no effect for these metrics. The differing responses may have been influenced by T. tubifex lineage differences. The habitat manipulations did not show sufficient promise to encourage further efforts in Colorado.