Patterns and dynamics of the salt marsh vegetation that surrounds many of the salt lake systems of arid/semi-arid Australia are poorly known. Lake Austin is a very large salt lake with extensive areas of fringing salt marsh; it is located in the arid Yilgarn Region of Western Australia. In this study, the changes in this vegetation over a 4-year period (1998–2002), during which both a major flooding event and addition of hypersaline groundwater from a nearby mining operation occurred, are reported. The monitoring program, based on Before-After-Control-Impact (BACI) principles, was designed to detect impacts of discharging hypersaline water into the lake; however, the flooding event, the result of above average rainfall in early 2000, complicated the results. The rains of 2000 and subsequent inundation of the vegetation immediately fringing the lake bed and major inlet channels resulted in dramatic changes to the species composition of annual and short-lived species and growth of perennial species. Flooding resulted in substantial death and damage to perennial shrubs (particularly Halosarcia fimbriata) due most likely to a combination of several weeks/months of inundation and smothering by macroalgae and Ruppia, with smaller plants and those closer to the lake bed impacted upon to a greater degree. Seed germination and recruitment of new Halosarcia plants was substantial as floodwaters receded with the majority of these seedlings surviving some 2 years after flooding despite the severe drought that followed the flood. Growth rates of seedlings differed substantially and were linked to subtle differences in micro-topography. Recruitment following flooding was also demonstrated in in vitro experiments involving inundated soil cores, provided water was relatively non-saline (conductivity \u3c30 mS cm−1). A conceptual model is proposed to explain changes in fringing vegetation in response to frequency, depth, period and salinity of flooding in relation to micro-topography. Despite the profound effect of flooding, impacts of discharge were identified, with changes in topsoil pH and salinity greater in areas closer to the discharge than those further away. Impacts on vegetation characteristics were not detected