The Malkumba-Coongie Lakes Ramsar Site has extensive terrestrial and freshwater ecosystems (largest Ramsar Site in Oceania, 2,178,952 ha, designated in 1987), including freshwater and salt lakes, lignum swamps and river channels in central Australia. It is supplied by Cooper Creek, a free-flowing Lake Eyre Basin river system. The area includes pastoral leases (97% of site grazed, including a regional conservation reserve (35%)) and a National Park (3%), with the largest oil and gas production field in Australia. We developed a Strategic Adaptive Management (SAM) Plan, linking science, monitoring and management of this social-ecological system, involving stakeholders and workshops. This involved developing a shared vision and hierarchy of objectives linked to management actions and identified outputs and outcomes. We exemplify this approach with explicit and measurable end-points (thresholds of potential concern) culminating from low level objectives for fish communities, particularly the alien sleepy cod Oxyeleotris lineolata. We describe this framework, highlighting the benefits in prioritizing management actions and monitoring in collaboration with a diverse range of stakeholders, driving adaptive feedback for learning. The whole approach is aimed at successfully achieving mutually agreed management objectives and the vision to maintain the ecological character of the Malkumba-Coongie Lakes Ramsar Site.