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Athalassic wetlands play a pivotal role in sediment and nutrient cycling and retention at the catchment level and are important ecosystems for local and regional biodiversity. Yet, the management of wetlands outside of riverine floodplains (non-riverine wetlands) is difficult, as there is limited understanding of these water bodies and of the processes that threaten them, like secondary salinisation. Accordingly, we describe the patterns of variation in wetland salinity and water chemistry across a regional landscape that is threatened by secondary salinisation. Spatial analyses indicated the distribution of the study wetlands was non-random and there was considerable positive spatial auto-correlation in water chemistry among wetlands—indicating a lack of independence. We detected massive variation in water chemistry among wetlands compared to minimal within-wetland variation and conductivity accounted for most of the among-wetland variation confirming its prominence in non-riverine wetland water chemistry. Wetland salinities were classified by their chemical evaporative pathway and we found a number of wetlands that may have become secondary salinised. The results reported here support the notion that the study, conservation and management of non-riverine wetlands should include assessments made at multiple spatial scales from individual waterbodies through to catchments. This is important because wetlands may not be independent units, but components of larger systems. However, we also note that the use of individual wetlands as units of replication may be problematic under some circumstances. We also argue that the identification of secondarily salinised wetlands will often require a multiple lines of evidence approach. [ABSTRACT FROM AUTHOR]