In natural karst systems, limestone diagenesis can be significantly influenced by bacterial activity in the soil horizon. Here, we investigate the effects of microorganisms on the elements migration of calcium and magnesium in karst soil systems by using different microbial treatments in simulated soil-limestone systems. Two bacterial strains, GLRT102Ca and JFSRT303 were specially studied. The leaching and release of Ca 2+ in the experiments was characterized by a rapid initial increase followed by a sharp decrease before a gradual approach to equilibrium. In contrast, the Mg 2+ concentrations in the leachates showed an initial decrease before a gradual approach to equilibrium. Microorganisms significantly promoted Ca 2+ and Mg 2+ migration in the simulated systems. The total amounts of Ca 2+ and Mg 2+ in leachates varied with microbial treatments. The soil+GLRT102Ca columns showed the highest total amount of Ca 2+ in leachates. This increased by a factor of 2.2 relative to the control columns. The highest total amount of Mg 2+ in leachates was presented in the soil+JFSRT303 columns, which leached 58.0% more total amounts of Mg 2+ than the control columns. The activities of a microbial specific enzyme, carbonic anhydrase (CA), present in the investigated columns were also examined. Varying levels of CA activities were detected in the leachates collected from soil columns with microbial activity. This suggests that the microbes in soil columns produced and released CA. The mean activity of CA in leachates was significantly correlated with total amount of Ca 2+ in leachates (r=0.86, P<0.01). This implied that microbially produced CA might be a major factor influencing Ca 2+ release and leaching in natural karst systems.