This paper describes a semi-quantitative approach for the assessment of sea-level rise (SLR) impacts on social-ecological systems (SES), using Yellow Water wetland on Kakadu National Park as a case study. The approach includes the application of a diagnostic framework to portray the existing SES configuration, including governance structures, in combination with qualitative modelling and Bayesian belief networks. Although SLR is predicted to cause saltwater inundation of freshwater ecosystems, cultural sites and built infrastructure, our study suggested that it may provide also an opportunity to bring together Indigenous and non-Indigenous knowledge and governance systems, towards a commonly perceived threat. Where feasible, mitigation actions such as levees may be required to manage local SLR impacts to protect important freshwater values. In contrast, adaptation will require strategies that facilitate participation by Kakadu Bininj (the Aboriginal people of Kakadu National Park) in research and monitoring programs that enhance understanding of salinity impacts and the adaptive capacity to respond to reasonably rapid, profound and irreversible future landscape-scale changes.