To assess the exposure of Blackfoot River mountain whitefish Prosopium williamsoni to the exotic parasite Myxobolus cerebralis, the cause of salmonid whirling disease, we investigated the spawning behavior of 49 adult mountain whitefish and their overlap with M. cerebralis within the Blackfoot River basin, Montana. A majority of the mountain whitefish radio‐tagged in the Blackfoot River migrated upstream (range, 0.1–79.0 km) to spawning sites located primarily in the main stem of the Blackfoot River. Spawning ranged from 31 October in the lower river to 9 November in the upper river and occurred across a range of substrate and channel types. Despite later spawning in the upper river, eggs hatched earlier under the warming influence of groundwater inflows. Here, a majority of wild mountain whitefish fry (65%) tested positive for M. cerebralis infection during the immediate posthatch period of mid‐April. Conversely, mountain whitefish fry from the lower river, downstream of the groundwater influence, showed no detectable infection. June exposure trials using surrogate rainbow trout Oncorhynchus mykiss in nine tributaries supporting mountain whitefish showed M. cerebralis infection rates ranging from 0% to 100% as well as a pattern of high triactinomyxon (TAM) exposure throughout the main‐stem Blackfoot River. For mountain whitefish, the co‐occurrence with M. cerebralis varied spatially across the basin and temporally within the main‐stem Blackfoot River at the most vulnerable early life stages. This variability appears to buffer age‐0 mountain whitefish from infectious conditions across large areas of the basin. However, continuous TAM release from groundwater‐influenced environments coinciding with mountain whitefish hatch and early rearing may impose pathogenic conditions on mountain whitefish in the upper Blackfoot River.

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Anthropogenic degradation of aquatic habitats has prompted worldwide efforts to improve or restore stream habitats for fisheries. However, little information exists on the long‐term responses of salmonids to restoration in North American streams. To recover wild trout populations in the Blackfoot River in western Montana, a collaborative approach to stream restoration began in 1990 to improve degraded stream habitats, primarily on private land. To assess the efficacy of various restoration techniques (channel reconstruction and placement of instream habitat structures, restoration of natural instream flows, installation of fish ladders and screens at irrigation diversions, and modification of grazing practices) in the recovery of wild trout, we examined long‐term (>5 years) trends in trout abundance on 18 tributaries treated between 1990 and 2005 and subsequently monitored between 1989 and 2010. At pretreatment conditions, average trout abundance was significantly lower in treatment versus reference sites (0.19 versus 0.62 trout/m; P = 0.0001). By 3 years posttreatment, trout abundance had increased significantly to an average of 0.47 trout/m across treatment sites (P = 0.01) and was no longer significantly different from the reference average (P = 0.12). These initial rapid increases were sustained over the long term (5–21 years) in 15 streams. However, trout abundance declined below pretreatment levels on three streams presumably due to the return of human impacts from heavy riparian grazing and detrimental irrigation practices. Although long‐term (12 year) average response trends were positive, trends varied spatially and native trout responded more strongly in the upper portion of the basin. Study results indicate that restoration should focus in the mid to upper basin and emulate features of natural channels to promote life history diversity and the recovery of native trout. Finally, long‐term monitoring led to adaptive management on most (10 of 18) projects, and thus proved vital to the overall sustainability of wild trout fisheries throughout the basin.

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.

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