It is possible that common earth-surface geological features can arise as a result of bacteria interacting with purely physical and chemical processes. The ability to distinguish ancient and modern mineral deposits that are biologically influenced from those that are purely abiotic in origin will advance our ability to interpret microbial evolution from the ancient rock record on earth and potentially other planets. We have combined carbonate mineralogical and geochemical environments together with community-based microbial genetic analyses in hot spring drainage systems at Mammoth Hot Springs in Yellowstone National Park. Previously (7), we reported the shape and chemistry of carbonate mineral deposits (travertine), that have formed along the hot spring pathways. This travertine exhibits five distinct ecological zonations (termed sedimentary facies) even though most physical and chemical attributes of the spring water change smoothly and continuously over the course of the drainage outflow path. Here, we document an unexpectedly sharp correlation between microbial phylogenetic diversity and travertine facies, which suggests that changes in bacterial community composition are a sensitive indicator of environmental conditions along the spring outflow. These results provide an environmental context for constraining abiotic and biotic theories for the origin of distinct crystalline structures and chemistries formed during hot spring travertine precipitation.