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This study is a taxonomic account describing 272 diatom taxa, from 50 genera, found in the meromictic lakes adjacent to the Gordon River and the Gordon River estuary in south-west Tasmania. The flora of the region includes cosmopolitan, tropical, Antarctic, Southern Ocean and uniquely Australian taxa in habitats ranging from fresh water to brackish and marine. Sampling sites were ordinated using Detrended Correspondence Analysis (DCA) and a direct correlation was found between their species composition and salinity. The taxonomic and iconographic sections include descriptions and illustrations of the taxa encountered as well as information on their autecology. This information has been applied in palaeolimnological investigations of sediment cores from Lake Fidler. These studies have provided a historical perspective on which recommendations for improved management of the Gordon River and its adjacent lakes have been based.