Rottnest Island, Western Australia, contains eight hypersaline lakes that became isolated from the Indian Ocean ~1,900 years ago. Distinctive facies include texturally diverse microbial mats, coated grains, spherulites, stromatolites and thrombolites, along with gypsum granules and crusts. Carbonate precipitates are restricted to littoral areas in the lakes, suggesting hyperalkaline groundwater discharging into the lakes plays a role in their formation. Microbial carbonates are predominantly aragonite, with minor high-Mg calcite and a poorly crystalline Mg-Si substance locally. Cyanobacterial fossils, carbonate geochemistry and the presence of Mg-Si substances demonstrate an intimate relationship between microbial metabolisms, carbonate mineral precipitation and microbialite textures.