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In 2011, a large, long-duration flood occurred on the regulated Missouri River following six decades without flooding. This study evaluated the effects of the flood on riparian forest structure and composition. In 2012, 168 forest sites sampled in 2006-2009 were resampled on five floodplain segments between Montana and Missouri, with 80 sampled again in 2013-2014. Changes in riparian forest area over 2006-2012, by age class and segment, were assessed using aerial imagery and GIS. Repeated-measures analysis of variance was used to examine (a) the initial effects of the flood (preflood to 2012) on tree and shrub stem densities, (b) postflood (2012-2014) changes in stem density, and (c) species-level responses for cottonwood (Populus deltoides), eastern red cedar (Juniperus virginiana), and Russian olive (Elaeagnus angustifolia). Across the study area, forest area declined 6-38% among age classes, with the greatest declines in the youngest classes. Tree density declined 19-49% across segments from preflood to 2012 but did not change significantly from 2012 to 2014. Shrub density declined 52-89% across segments from preflood to 2012, with 73-78% declines in the two youngest age classes, but increased by 42% from 2012 to 2014. Cottonwood and Russian olive, but not red cedar, showed partial recovery in the shrub/sapling layer, increasing from 2012 to 2014. Although flooding is important for floodplain forest health, the 2011 flood had mixed effects, with significant mortality of native floodplain trees and shrubs and only limited cottonwood recruitment. The initial decline in invasive species (Russian olive and red cedar), however, suggests that flooding may be an effective management tool.