The internationally important river–floodplains of the Kakadu Region in northern Australia are at risk from invasive species and future sea-level rise–saltwater inundation (SLR–SWI), requiring assessments of multiple cumulative risks over different time frames. An integrated risk-assessment framework was developed to assess threats from feral animals and aquatic weeds at three SLR-scenario time frames (present-day, 2070 and 2100) to natural (magpie goose habitats), cultural (indigenous hunting–fishing sites) and economic (tourism revenue less invasive species control costs) values. Probability density functions (pdfs) were fitted to spatial data to characterise values and threats, and combined with Monte Carlo simulation and sensitivity analyses to account for uncertainties. All risks were integrated in a Bayesian belief network to undertake ‘what if’ management-scenario analyses, and incorporated known ecological interactions and uncertainties. Coastal landscapes and socio-ecological systems in the region will be very different by 2100 as a result of SLR; freshwater ecosystems will transform to marine-dominated ecosystems and cannot be managed back to analogue conditions. In this context, future invasive-species risks will decrease, reflecting substantial loss of freshwater habitats previously at risk and a reduction in the extent of invasive species, highlighting the importance of freshwater refugia for the survival of iconic species.