The Bonneville Basin is a continental lacustrine system accommodating extensive microbial carbonate deposits corresponding to two distinct phases: the deep Lake Bonneville (30 000 to 11 500 14C bp) and the shallow Great Salt Lake (since 11 500 14C bp). A characterization of these microbial deposits and their associated sediments provides insights into their spatio‐temporal distribution patterns. The Bonneville phase preferentially displays vertical distribution of the microbial deposits resulting from high‐amplitude lake level variations. Due to the basin physiography, the microbial deposits were restricted to a narrow shoreline belt following Bonneville lake level variations. Carbonate production was more efficient during intervals of relative lake level stability as recorded by the formation of successive terraces. In contrast, the Great Salt Lake microbial deposits showed a great lateral distribution, linked to the modern flat bottom configuration. A low vertical distribution of the microbial deposits was the result of the shallow water depth combined with a low amplitude of lake level fluctuations. These younger microbial deposits display a higher diversity of fabrics and sizes. They are distributed along an extensive ‘shore to lake’ transect on a flat platform in relation to local and progressive accommodation space changes. Microbial deposits are temporally discontinuous throughout the lake history showing longer hiatuses during the Bonneville phase. The main parameters controlling the rate of carbonate production are related to the interaction between physical (kinetics of the mineral precipitation, lake water temperature and runoff), chemical (Ca2+, Mg2+ and HCO3− concentrations, Mg/Ca ratio, dilution and depletion) and/or biological (trophic) factors. The contrast in evolution of Lake Bonneville and Great Salt Lake microbial deposits during their lacustrine history leads to discussions on major chemical and climatic changes during this interval as well as the role of physiography. Furthermore, it provides novel insights into the composition, structure and formation of microbialite‐rich carbonate deposits under freshwater and hypersaline conditions.