Freshwater coastal wetlands in Northern Australia are experiencing severe impacts from saltwater intrusion as a result of sea level rise. This study examined the impact of increasing salinity using sediment cores collected from nine wetlands, in three floodplains between Darwin and Kakadu in the Northern Territory, Australia. The sediment cores were inundated with one of four treatment salinities ranging from freshwater (0ppt) to seawater (35ppt). The changes to the abundance and species richness of aquatic invertebrates and macrophytes, and the abundance of phytoplankton and benthic algae were analysed. Benthic algal biomass, phytoplankton concentration, macrophyte and macroinvertebrate abundance and species richness were all negatively correlated with salinity. Benthic algae form the basis of aquatic food webs in Northern Australia and as such, reductions in biomass production due to increased salinity has the potential to impact the production of higher trophic level organisms in freshwater coastal wetlands and the wider floodplain ecosystem. The loss of food resources including algae and aquatic invertebrates due to sea level rise is hypothesised to cause trophic cascades in coastal freshwater wetlands of Northern Australia.