System dynamics modelling is an underutilized tool that can provide flexible and system-response analyses of environmental flows. Because system dynamics models are able to incorporate causal connections between social, economic and environmental aspects of a system, they are well suited to study water management problems. In addition, system dynamics models are excellent tools for incorporating expert and stakeholder feedback, which is an important component of any environmental flow study. Given the benefits of using a system dynamics modelling approach, our objective was to develop and demonstrate a stochastic system dynamics modelling framework to evaluate environmental flow alternatives. Specifically, our research examined the influence of flow alternatives on cottonwood recruitment and reservoir storage within the Rio Chama basin, New Mexico, USA. We used the ‘recruitment box model’ to investigate the impact of three alternatives on cottonwood recruitment within the project reach. The recruitment box model attributes seedling survival to floodplain elevation, annual timing of peak flows and river stage declines that match seedling root growth. We also demonstrate how flow alternatives can be evaluated using comparative metrics, which allow water resource managers to more easily evaluate alternatives before incorporating environmental flows into existing operations. Copyright © 2014 John Wiley & Sons, Ltd.