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Riparian cottonwood (Populus deltoides) forests form the one of the most extensive deciduous forest ecosystems in arid regions of the western United States. However, cottonwood populations are threatened by flow alteration and channel degradation caused by dams, water diversions, and groundwater pumping. We developed a stochastic, density-dependent, population model to (1) consolidate information concerning cottonwood population dynamics in a conceptual and analytical framework, (2) determine whether complex forest stand dynamics can be predicted from basic cottonwood vital rates and river hydrology, and (3) aid in planning prescribed floods by projecting how altered flow regimes might affect populations. The model describes how annual variation in the hydrograph affects cottonwood mortality (via floods and droughts) and recruitment (via scouring of new habitat and seedling establishment). Using parameter values for the undammed Yampa River in Colorado, we found that abundances of seedlings and younger trees followed a boom–bust cycle driven by high flood mortalities while reproductive adult abundance followed a less erratic 5–15-yr periodicity driven by multiyear sequences of flows favorable to stand recruitment. Conversely, chance occurrences of multiple drought years eliminated cottonwood from up to 50% of available habitat, providing opportunities for competing plant species to establish. By simulating flow alterations on the Yampa ranging from channelization (many floods/droughts) to damming (few floods/droughts), the model suggested that mature cottonwood forest should be most abundant near the observed natural flow regime. Model analysis also suggested that flow regimes with high flood frequencies result in stable (albeit small) population sizes, while stable flows result in highly variable population sizes prone to local extinction.