Microbes that play an important role in calcium carbonate deposition, but whose details are not well known, were studied. The Shijiangjun cave in the midwest of Guizhou province was chosen as the source for carbonate depositing bacteria separation as it has been investigated with respect to geology and geomorphology, and has been monitored for years for dripping water hydrogeochemical parameters. Samples of microorganisms collected from the cave sediment surface were separated by a B-4 culture medium, which is a common oligotrophic medium for carbonate depositing bacteria separation. B-4C medium (added Mg²⁺) was used for analysis of the Mg impact in the system. Fifty-eight strains were separated from eight samples, and finally, five strains that showed significant deposition phenomena were chosen for the liquid deposition test. The pH and Ca and Mg concentration in the system before and after the liquid deposition test were monitored. The mineral composition and morphology of the CaCO₃ crystals filtered from the liquid deposition test system were analyzed using an X-ray diffraction analyzer (XRD) and a scanning electron microscope (SEM), respectively. The XRD results show that three carbonate compositions were found in the B-4 medium liquid system (without Mg²⁺): calcite, calcite-vaterite mixture, and vaterite. The composition seems to have been affected by the pH. There was no aragonite in the liquid system, and thus, the factors causing the formation of aragonite stalagmite need future research. Mg has been considered to be a participant in the formation of aragonite stalagmite, but it was not affected in this research. SEM pictures show the morphology of different carbonate crystals, including irregular hexagonal polytypes, cylindrical objects, square layers, and hemispherical types. These are rarely reported in the chemical system. Moreover, bacteria-shaped holes were observed on the crystal surface, implying the involvement of microbes in the deposition process.