Diatom and micro-invertebrate communities were analyzed in 56 lentic wetlands from the wheatbelt of Western Australia. Sixteen water quality parameters were measured at each habitat and were tested as determinants of diatom and micro-invertebrate distribution. Nearly all waters were dominated by Na1+ and Cl1- and over half had low buffering capacity (<2 meq/L as TCO32-). Salinities ranged from < 1 to > 240 mS/cm; some hypersaline habitats had pH values as low as 2.1, but most sites were alkaline. Diatoms (165 taxa) were present in all habitats, with indications that assemblages are correlated with land-use practices, i.e., historical clearing of native vegetation for dryland agriculture with resultant hydrological problems of salinization and water-logging. A non-metric multidimensional ordination showed pH, salinity, TCO32-, 3, and total phosphorus to be significantly correlated with diatom community structure. Principal components analysis showed similar patterns. A salinity index was also developed for numerically important diatom taxa. Principal components analysis showed similar patterns. Certain tolerant Bacillariales, including Hantzschia amphioxys, Nitzschia hybrida, Tryblionella hungarica, and N. recta, were numerically important taxa in wetlands with visible signs of salinization. Micro-invertebrates (143 taxa) were present in habitats with salinities up to 200 mS/cm. Multidimensional ordinations showed salinity to be significantly correlated with micro-invertebrate community structure. The cladoceran Daphniopsis queenslandensis, ostracods Australocypris insularis, Mytilocypris tasmanica chapmani, and Platycypris baueri, and copepods Apocyclops dengizicus and Mesochra nr. flava were numerically important micro-invertebrates in moderate to high salinity environments, including those with signs of salinization. The diatoms, Navicula minuscula var. muralis and Pinnularia divergentissa var. subrostrata, and the copepod, Calamoecia trilobata, were common inhabitants of the extreme hypersaline (greater than or equal to75 mS/cm), acidic (<4) habitats. Diatom communities were similar to those previously reported for other regions in Australia subjected to salinization; there were some differences in micro-invertebrate communities.