To assess the exposure of Blackfoot River rainbow trout Oncorhynchus mykiss to the exotic parasite Myxobolus cerebralis, the causal agent of whirling disease, we investigated the spawning life histories of adult rainbow trout with respect to the distribution and severity of infection in spawning and early rearing areas in two distinct reaches of the Blackfoot River. Radiotelemetry confirmed that Blackfoot River rainbow trout express a fluvial life history and migrate from wintering sites within the Blackfoot River to spawning sites in the lower reaches of tributaries. Spawning peaked in late April, and fry emergence was estimated to occur within a narrow window of time in early July during the known period of high parasite exposure. However, the severity of infection varied between study reaches. Spawning of lower Blackfoot River rainbow trout was dispersed among the lowermost reaches of smaller, colder, higher-gradient tributaries, most of which fell below our ability to detect infection. By contrast, a majority of the telemetered rainbow trout in the middle Blackfoot River spawned higher in the drainage and within a single, low-gradient stream where fry emerged under infectious conditions. For fluvial rainbow trout, the risk of infection varies from the tributary to the subbasin scale and relates to the geographical arrangement and properties of the tributaries, the longitudinal relationship of the pathogen to spawning and early rearing areas, and the rate and timing of dispersing age-0 fry to downstream parasite-positive waters. Before the introduction of M. cerebralis, the middle Blackfoot River was identified as having recruitment limitations caused by winter mortality and anthropogenic activities. According to our results, riparian restoration and habitat enhancement with emphasis on migratory native fish within and upstream of the pathogen may buffer fish from the effects of the disease.