1. The effect of increasing salinity on the emergence of zooplankton eggs and the germination of aquatic plant seeds from the sediment of two wetlands was examined. Salinity was found to cause reductions in species richness and abundance of aquatic plants and zooplankton at salinities between 1000 and 5000 mg L−1. Aquatic plants also had an associated decrease in above ground biomass.2. Individual taxa showed different responses to salinity, and four response patterns were identified: (i) increased number of organisms emerging at 1000 mg L−1; (ii) decreased number of organisms emerging above 1000 mg L−1; (iii) decreased number of organisms emerging between 300 and 1000 mg L−1; (iv) no difference in number of organisms emerging across the range of salinities. Response patterns (iii) and (iv) were common to both plants and zooplankton, whereas response patterns (i) and (ii) were only identified for zooplankton.3. Results indicate that there is potential for the increasing salinity in Australian rivers and wetlands to decrease the species richness of aquatic communities resulting in loss of wetland biodiversity.