Climate change is likely to impact on coastal and lowland areas of Kakadu National Park through rising sea levels and saltwater inundation. Kakadu National Park is managed under a joint management arrangement; a partnership between Bininj/Mungguy and the Australian Government which enables Bininj/Mungguy to look after their country in cooperation with staff of the Kakadu National Park. This case study looks at modelling of the river system hydrodynamics to assess the risk of saltwater intrusion and extreme rainfall events on low-lying coastal wetlands of the South Alligator River catchment, and to discuss the implications of government planning, management and policy responses. Key opportunities exist to use the methodologies and processes from this study, and capture the findings in future planning and government decision making processes.