The Great Basin included several lacustrine systems that accommodated extensive carbonate buildups: the Lahontan on the western side (dating back to 48 kyr cal bp), and the Bonneville (from 30 to 11.5 kyr cal bp) and Great Salt Lake (starting 11.5 kyr cal bp) on the eastern side of the basin. The eastern lakes show a transition from freshwater to hypersaline conditions. In contrast, the western lakes do not show any significant change from the originally prevailing freshwater conditions. Mapping of the carbonate buildups in the different lakes settings enables a comparison of a biotic versus an abiotic composition of the carbonate buildups, their morphologies and their specific spatial distributions. The morphology, size and distribution of the carbonate deposits are predominantly governed by seasonal to long-term water level fluctuations, particular geomorphological heritage, fault-induced processes, groundwater seepage and substrates. All of the lakes show a palaeoshoreline distribution with some buildups containing crusts, hemispheroid domes, and parts of complex domes resulting from climate-induced lake level variations. However, the presence of columns and complex domes made up of mixed biotic/abiotic carbonates in the western Great Basin is related to the influx of groundwater. Winnemucca Lake and Pyramid Lake contain bigger buildups than the ones observed in the eastern Great Basin lakes. The presence of these large size buildups and thinolites in the Lahontan lacustrine system are a consequence of local hydrological processes associated with influenced groundwater flows through specific sedimentary structures (for example, from springs and delta fronts) and faults. This contrast in the distribution, composition and size of the buildups between the two sides of the Great Basin suggests local changes in water chemistry (for example, [Ca2+]) and groundwater influxes. This work provides a novel conceptual model for the formation of abiotic and/or biotic carbonate buildups in lacustrine settings.