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Sedimentary facies and stratigraphic architecture of non-marine carbonates are controlled by a range of environmental parameters, such as climate, hydrology and tectonic setting, but the few published facies models do not account for this variability. Outcrop and petrographic observations from the Mupe Member of the Purbeck Limestone Group (Upper Jurassic-Lower Cretaceous) in Dorset, southern England, are the basis for new depositional models of non-marine microbialites and associated carbonates in an extensional basin. Ten facies are defined, described and grouped into five facies associations. The Mupe Member is characterised by accumulation of in situ microbial mounds developed around tree remains preserved as moulds and silicified wood. Mounds occur within three stratigraphic units, separated by three palaeosoils, characterised by less-porous, bedded, inter-mound packstone-grainstone that commonly onlap mound margins. Mounds are developed mainly in the shallowest areas of the lake, as indicated by their shapes, facies relationships and association with palaeosoils. These microbial mounds are compared to modern (Laguna Bacalar, Mexico and Great Salt Lake, Utah, USA) and ancient (Eocene Green River Formation, Uinta Basin, Utah, USA) analogues to assess their value as palaeoenvironmental indicators. Facies transitions indicate an earlier, brackish-water lake and a later hypersaline lake for the Mupe Member, both within a semi-arid climate setting in an extensional basin. The fact that the microbialites are covered by evaporitic strata, together with sedimentological, palaeontological and stable isotope data, suggest that there was a sharp change from through-flowing brackish-water, to a closed hypersaline, lacustrine system.