The natural Australian landscape sustains a mosaic of wetlands that range from permanently wet to temporary. This diversity of wetland types and habitats provides for diverse biotic communities, many of which are specific to individual wetlands. This paper explores the prospects for southern Australian wetlands under modified water regime and salinity induced by climatic changes. Extended droughts predicted as a consequence of climate change (lower rainfall and higher temperatures) combined with human-induced changes to the natural hydrological regime will lead to reductions in the amount of water available for environmental and anthropogenic uses. Reduced runoff and river flows may cause the loss of some temporary wetland types that will no longer hold water long enough to support hydric communities. Species distributions will shift and species extinctions may result particularly across fragmented or vulnerable landscapes. Accumulation of salts in wetlands shift species-rich freshwater communities to species-poor salt tolerant communities. Wetlands will differ in ecological response to these changes as the salinity and drying history of each wetland will determine its resilience: in the short term some freshwater communities may recover but they are unlikely to survive and reproduce under long term increased salinity and altered hydrology. In the long term such salinized wetlands with altered hydrology will need to be colonized by salt tolerant species adapted for the new hydrological conditions if they are to persist as functional wetlands. As the landscape becomes more developed, to accommodate the need for water in a warmer drying climate, increasing human intervention will result in a net loss of wetlands and wetland diversity.