Flow variability plays a central role in structuring the physical environment of riverine ecosystems. However, natural variability in flows along many rivers has been modified by water management activities. We quantified the relationship between flow and establishment of the dominant tree (plains cottonwood, Populus deltoides subsp. monilifera) along one of the least hydrologically altered alluvial reaches of the Missouri River: Coal Banks Landing to Landusky, Montana. Our purpose was to refine our understanding of how local fluvial geomorphic processes condition the relationship between flow regime and cottonwood recruitment. We determined date and elevation of tree establishment and related this information to historical peak stage and discharge over a 112-yr hydrologic record. Of the excavated trees, 72% were established in the year of a flow >1400 m³/s (recurrence interval of 9.3 yr) or in the following 2 yr. Flows of this magnitude or greater create the necessary bare, moist establishment sites at an elevation high enough to allow cottonwoods to survive subsequent floods and ice jams. Almost all cottonwoods that have survived the most recent flood (1978) were established >1.2 m above the lower limit of perennial vegetation (active channel shelf). Most younger individuals were established between 0 and 1.2 m, and are unlikely to survive over the long term. Protection of riparian cottonwood forest along this National Wild and Scenic section of the Missouri River depends upon maintaining the historical magnitude, frequency, and duration of floods >1400 m³/s. Here, a relatively narrow valley constrains lateral channel movement that could otherwise facilitate cottonwood recruitment at lower flows. Effective management of flows to promote or maintain cottonwood recruitment requires an understanding of locally dominant fluvial geomorphic processes.