Small alpine water bodies can play a large role in defining patterns of biological and landscape diversity, and may be particularly sensitive to climate change. A large limnological dataset, consisting of 65 and 6 water bodies, respectively, on South Island and Stewart Island (New Zealand) and 76 and 12 water bodies, respectively, in the Tasmanian highlands and coastal areas (Australia), was constructed to assess patterns of variation in alpine and subalpine lakes in the Australasian region. With the exception of the coastal systems, most lakes were very dilute. In general, lake water chemistry resembled world average seawater cationic ratios (WASW). In addition, some New Zealand lakes fell close to the world average freshwater cationic ratios (WAFW), due to relatively high calcium concentrations, and some were dominated by magnesium due to the presence of serpentine bedrock in the catchment area. Multivariate analyses of the joint dataset revealed that the variation in chemical limnological variables was dominated by gradients in conductivity, pH and gilvin. The concurrent relationships between pH, calcium and gilvin, which enabled the differentiation of Tasmanian water bodies into limnological provinces, were absent in New Zealand. In the latter, pH and gilvin contents were not coincident, as clear-water acidic systems occurred in New Zealand. The higher diversity of freshwater bodies in New Zealand will enable independent assessment of the effects of pH and gilvin on the distribution and diversity of biota.