Multiple abiotic and biotic factors combine in nature to influence the formation of calcium carbonate limestone deposits. Systems Geobiology studies of how micro-organisms respond to, or sometimes even control, the coupled effects of environmental change and mineralization will permit more accurate interpretation of the fossil record of ancient microbial life. Mammoth Hot Springs in Yellowstone National Park, USA, serves as a natural laboratory for tracking how the dynamic interplay of physical, chemical and biological factors come together to form hot-spring limestone (called ‘travertine’). Systematic downstream correlations occur at Mammoth Hot Springs between travertine deposition (geomorphology, crystalline structure and geochemistry), microbial communities (mat morphology, pigmentation, and phylogenetic and metabolic diversity) and spring-water conditions (temperature, pH, geochemistry and flow). Field-based microscale and mesoscale experimentation indicates that microbes directly influence travertine growth rate and crystalline structure. At the macroscale, time-lapse field photography and numerical modelling suggest that travertine terrace geomorphology is influenced strongly by hydrology, heat dispersion and geochemistry. These results from Mammoth Hot Springs allow establishment of a conceptual framework across broad spatial and temporal scales in which to track how multiple geological and biological factors combine to control CaCO3 crystal precipitation and the resulting formation of travertine deposits.