Diatom diversity of six small playa lakes within the Yarra Yarra drainage system, Western Australia, and the environmental variables likely to influence their distribution was investigated. Thirty-one pennate diatom taxa were identified. Taxa consisted of facultative planktonic and periphytic, circumneutral to alkaliphilous or pH-indifferent forms with known adaptations to saline conditions and fluctuations in salinity in NaCl dominated waters. Data were analysed by ordination (MDS and PCA), hierarchical clustering (CLUSTER), permutation-based hypothesis testing (ANOSIM) and comparative tests on similarity matrices (RELATE). Water depth accounted for the majority of variation in the environmental data. REALTE comparisons of environmental and taxa data did not produce a significant correlation value. We propose that the poor concurrence of the datasets was influenced by the wide ecological tolerances of the taxa recorded, some crucial unmeasured environmental variable/s, possible geographical regionalisation and/or unsampled taxa variability owing to the stochastic nature of the wetlands. Broad patterns of distribution were related to hydroperiod and some taxa groups were loosely associated with environmental groups consistent with established ecological tolerances for the taxa.