Records of the past climate and vegetation of Australia are frequently constructed using data generated from the analysis of pollen and pteridophyte spores alone, or in association with sedimentology. We demonstrate that the organic residue prepared for pollen analysis yields other organic-walled microfossils that can be used to provide additional and independent palaeoenvironmental information. These non-pollen palynomorphs (NPP) include microscopic remains of algae, cyanobacteria, fungi, insects, other invertebrates and cormophytes. Our study of the NPP from two Late Quaternary lake records from western Victoria, Australia, provided additional information on water quality, salinity, depth, temperature and nutrient levels to the general environmental interpretation derived from pollen data. From a review of the ecological preferences of taxa, and comparison of the NPP results with pollen and spore curves from the lake records, ecological indicator values were derived. The study confirms the utility of NPP in enhancing environmental reconstructions in Australia, and encourages their routine examination in palynological studies.