Lakes in arid and semi-arid regions respond to climatic change through shifts in lake water volume and ionic concentration. Because diatom distribution is highly correlated with lake hydrochemistry, diatoms can be used to infer changes in salinity and brine composition and thus to infer past climates. Here we critically examine the use of diatom-inferred salinity as a climate proxy, with examples taken from both modern waterbodies and sedimentary profiles. Sediment records may contain assemblages mixed from periods or sites of differing hydrochemistries because of the high degree of spatial and temporal heterogeneity in saline systems. Dissolution and diagenesis in saline brines may further complicate interpretation of sedimentary assemblages. Furthermore threshold effects, salinity regulation via groundwater seepage, antecedent conditions, and other aspects of local hydrology may modify the relationship between salinity change and climatic forcing. These complexities necessitate critical examination of the ecology and taphonomy of sedimentary assemblages, as well as evaluation of potential non-linearities in the salinity/climate relationship through comparison of diatom-inferred salinity with other proxy records of hydrochemical change, historical documents where they exist. and with other regional lake systems.