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Smolts of spring Chinook salmon Oncorhynchus tshawytscha experience substantial mortality while migrating through free-flowing reaches of the Snake River basin before reaching Lower Granite Dam, the first dam encountered in the Columbia-Snake river hydrosystem. We investigated the patterns of travel time and survival of hatchery and natural smolts fitted with passive integrated transponder (PIT) tags through specific reaches of the migration corridor during the 2000-2006 migration years for two populations originating in the Grande Ronde River basin (Lostine River and Catherine Creek). For both populations, median travel times for natural smolts were significantly longer in the upper reaches of the migration corridor but shorter in the lower reaches than for their hatchery counterparts. Also, among both hatchery and natural smolts, smaller individuals spent more time in the upper reaches, presumably feeding to attain a larger size before continuing their migration. Within populations, both hatchery and natural smolts showed similar patterns of survival through the reaches of the migration corridor above Lower Granite Dam. Size-selective mortality was evident for hatchery and natural smolts from both populations, especially in the upper reaches, larger individuals experiencing higher survival. The Catherine Creek population experienced the majority of natural and hatchery smolt mortality (32.8-65.8%) in a relatively short (91-km), low-gradient reach immediately below the summer rearing habitat. In contrast, the Lostine River natural and hatchery smolts experienced lower mortality (3.6-46.1%) in a 174-km reach below the summer rearing habitat. The results of this study demonstrate the dynamic nature of survival and migration rate among spring Chinook salmon smolts during their initial seaward migration from tributaries.

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Habitat degradation has been implicated as a primary threat to Pacific salmon Oncorhynchus spp. Habitat restoration and conservation are key toward stemming population declines; however, winter microhabitat use and suitability knowledge are lacking for small juvenile salmonids. Our objective was to characterize microhabitat use and suitability for spring Chinook Salmon Oncorhynchus tshawytscha parr during fall and winter. Using radiotelemetry techniques during October–February (2009–2011), we identified fall and winter microhabitat use by spring Chinook Salmon parr in Catherine Creek, northeastern Oregon. Tagged fish occupied two distinct gradient reaches (moderate and low). Using a mixed‐effects logistic regression resource selection function (RSF) model, we found evidence that microhabitat use was similar between free‐flowing and surface ice conditions. However, habitat use shifted between seasons; most notably, there was greater use of silt substrate and areas farther from the bank during winter. Between gradients, microhabitat use differed with greater use of large wood (LW) and submerged aquatic vegetation in the low‐gradient reach. Using a Bayesian RSF approach, we developed gradient‐specific habitat suitability criteria. Throughout the study area, deep depths and slow currents were most suitable, with the exception of the low‐gradient reach where moderate depths were optimal. Near‐cover coarse and fine substrates were most suitable in the moderate‐ and low‐gradient reaches, respectively. Near‐bank LW was most suitable throughout the study area. Multivariate principal component analyses (PCA) indicated co‐occurring deep depths supporting slow currents near cover were intensively occupied in the moderate‐gradient reach. In the low‐gradient reach, PCA indicated co‐occurring moderate depths, slow currents, and near‐bank cover were most frequently occupied. Our study identified suitable and interrelated microhabitat combinations that can guide habitat restoration for fall migrant and overwintering Chinook Salmon parr in Catherine Creek and potentially the Pacific Northwest.