Secondary salinisation has affected large areas of inland southwestern Australia, and in particular, low lying aquatic areas; causing the loss of freshwater submerged macrophyte communities and their replacement by salt-tolerant species. At high salinities, the salt-tolerant macrophyte-dominated ecological regime may be replaced by a regime dominated by benthic microbial communities, further reducing the structural and functional diversity of salinised wetland ecosystems. There is little prospect of restoring salinised systems to a freshwater state, meaning that saline macrophyte dominated wetlands have a heightened structural and functional importance in this landscape. Prior to this study, little was known about the drivers for change from one ecological regime to another in salinising wetlands or about rates of ecosystem response to these drivers. This study used experimental and observational data from seven saline wetlands in order to identify some of the potential mechanisms for the transition between the salt tolerant submerged macrophyte-dominated regime and the benthic microbial community-dominated regime. The applicability of existing conceptual models for ecological regime shifts was then tested against these data. Some of the mechanisms responsible for the formation and maintenance of the macrophyte-dominated regime were explored by examining the effects of salinity on germination and flowering in a series of salt-tolerant submerged macrophytes. The initiation and dominance of benthic microbial communities over a range of salinity and wetting regimes was also examined. The results suggested that macrophyte communities are unlikely to develop in seasonally-drying wetlands at high salinities (>45 ppt), but will usually germinate and establish well at lower salinities. It was also predicted that although benthic microbial communities can survive and grow across a wide range of salinities, they are likely to be outcompeted at low salinities by macrophytes or by phytoplankton blooms if water column nutrient levels are high. However, water permanence may facilitate benthic microbial community dominance. Existing conceptual models of ecological regime transitions, such as the alternative regimes model, did not account for the effect of water regime on the dynamics of seasonally-drying systems. Therefore, a new conceptual model incorporating the interaction between hydrology and salinity in seasonally-drying wetlands was proposed.