This paper provides an introduction to the ecological features that characterise the wetlands of the Kakadu region in northern Australia and places these in a wider context for other papers in a special issue that expands on these features. The special issue aims to (1) synthesise knowledge of the ecosystem process that underpins the management of the rivers and floodplains and (2) undertake an integrated assessment so as to evaluate alternative management responses in the face of an uncertain future. These aims are addressed in individual papers. The managerial and physical settings of the region are introduced before some of the previous wetland research is summarised and gaps in information considered. The gaps included an understanding of the relationship between the provision of ecosystem services and outcomes for water quality and biodiversity, and ecosystem and population dynamics of wetland biodiversity. In a conclusion, the occurrence and acceptance or management of invasive species is considered in terms of the emergence of novel ecosystems as a consequence of global change, in particular sea-level rise and anticipated transition of freshwater wetlands to saline conditions.