Flow regulation has significantly altered hydrological, geomorphic, and ecological processes on the Missouri River. Cumulative effects are evident in reductions in plains cottonwood (Populus deltoides) recruitment, altered forest age structure and species composition, losses of sandbar and shallow water habitat, and declines in sandbar-nesting birds and large river fishes. Although a national scientific panel recommended restoration of fluvial geomorphic processes to address these problems, management constraints have limited process-based restoration. Record runoff in 2011 exceeded reservoir capacity on the upper Missouri, leading to the highest flows in 59 years and exceptionally long flood durations (up to 3 months). We assessed the effects of this "large infrequent disturbance" by comparing pre- (2006-2009) to post-flood (2012) changes in riparian forests along six segments of the Missouri River. Live shrub and tree density declined sharply within young forest stands (<30 years). Higher proportions of non-native (Elaeagnus angustifolia) and upland (Juniperus virginiana) trees showed evidence of recent mortality than did the native cottonwood. Sandbar area increased sharply from 2006-2012 and area of young forests declined, with particularly strong declines in sapling stands that had established following the previous post-dam record flow releases in 1997. Cottonwood recruitment was widespread in 2012, but most seedling patches were on sandbars in the active channel, rather than on overbank sites. Physical and operational constraints within the regulated Missouri River limited the restorative effects of the 2011 flood and are likely to limit future forest recovery. Process-based restoration of ecosystem structure and function would require restoration of flow and sediment regimes that more closely mimic historical conditions, as well as overcoming the physical legacies of decades of flow regulation.