We developed a mass balance flow model to reconstruct unregulated daily peak flows in the National Wild and Scenic reach of the Missouri River, Montana. Results indicated that although the observed frequency of large peak flows has not changed in the post-dam period, their magnitude has been reduced from 40 to 50% as a consequence of flow regulation. Reductions in the magnitude of these flows should reduce the expected frequency of large flood-pulses over a longer time-scale. Results of a two-dimensional hydraulic model indicated that limited cottonwood (Populus deltoides subsp. Monilifera) recruitment occurs at relatively small peak discharges, but to maximize establishment of cottonwoods in the Wild and Scenic reach, a threshold of 1850 m³/s would be necessary at the Virgelle gauge. Floods of this magnitude or greater lead to establishment of cottonwood seedlings above the zone of frequent ice-drive disturbance. Restoring the frequency, magnitude, duration and timing of these flood pulses would benefit important natural resource values including riparian cottonwood forests and native fish species in the upper Missouri River basin. However, efforts to naturalize flow must be made in the context of a water management system that was authorized and constructed for the primary purposes of flood control, power generation and irrigation. Using the synthesized flow model and flood damage curves, we examined six scenarios for delivering flows ≥1850 m³/s to the Wild and Scenic reach. Whereas some scenarios appeared to be politically and economically infeasible, our analysis suggested that there is enough operational flexibility in the system to restore more natural flood pulses without greatly compromising other values.