Newly protected areas often have land-use legacies that affect their capacity to deliver conservation outcomes into the future. The management actions required to achieve conservation outcomes may be uncertain. This uncertainty may be resolved through experimental adaptive management that draws on knowledge of the ecology and history of the ecosystem. In New South Wales, Australia, river red gum (Eucalyptus camaldulensis) floodplain forests were gazetted as National Park in 2010, including Murray Valley National Park. Land-use legacies had resulted in one-third of river red gum forests and woodlands occurring as high-stem-density (>400stemsha-1) stands at the time of gazettal. High-stem-density stands are characterised by dominance of narrow straight trees, a paucity of large and hollow-bearing trees, modified understorey vegetation and reduced coarse woody debris. A simple state-and-transition process model captured knowledge of the processes that led to the high-stem-density river red gum forest state being widespread. We describe the establishment of a manipulative experiment to evaluate whether ecological thinning can achieve conservation outcomes in high-stem-density stands of river red gum floodplain forest. The experiment was designed to reduce intrastand competition for water and other resources, and encourage development of spreading tree crowns. Future results will inform management decisions in high-stem-density stands of river red gum floodplain forests. The adaptive management approach employed provides a template for using knowledge of the ecosystem to resolve uncertainty about management, particularly in newly protected areas.