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Alternative-states theory commonly applied, for aquatic systems, to shallow lakes that may be dominated alternately by macrophytes and phytoplankton, under clear-water and enriched conditions, respectively, has been used in this study as a basis to define different states that may occur with changes in wetland salinity. Many wetlands of the south-west of Western Australia are threatened by rapidly increasing levels of salinity as well as greater water depths and permanency of water regime. We identified contrasting aquatic vegetation states that were closely associated with different salinities. Salinisation results in the loss of freshwater species of submerged macrophytes and the dominance of a small number of more salt-tolerant species. With increasing salinity, these systems may undergo further change to microbial mat-dominated systems composed mostly of cyanobacteria and halophilic bacteria. The effect of …