Heavy metal pollution management is a global environmental problem that poses a great threat to the ecological environment. Adsorption and biomineralization are considered to be the two most promising heavy metal pollution remediation techniques among the numerous available ones. In this work, a combined heavy metal removal system was constructed employing the adsorption of montmorillonite and the mineralization of carbonate mineralizing bacteria to expand their application potential for controlling heavy metal water pollution. Analysis of changes in pH, CO32− concentration, Pb2+ concentration in the liquid phase, and changes in microscopic morphology, mineral phase, and functional group on sedimentary minerals was done to study the retention and fixation behaviour of montmorillonite and carbonate mineralizing bacteria on Pb2+. The results show that the liquid phase pH may be slightly altered by the ions dissolved in montmorillonite. Based on the conditions of montmorillonite and carbonate mineralizing bacteria functioning separately, the elimination of Pb2+ may reach 35.31% and 45.75%, respectively. However, when montmorillonite is combined with carbonate mineralizing bacteria, which is the heavy metal removal system constructed in this study, montmorillonite can buffer part of the Pb2+ rapidly and reduce its biotoxicity. Subsequently, these buffered Pb2+ are gradually desorbed by carbonate mineralizing bacteria and removed by the effect of mineralized deposition. Results from SEM, FTIR, and XRD indicate that Pb2+ is primarily removed from the liquid phase as rod-shaped PbCO3. It is worth noting that this process is able to significantly increase the removal of Pb2+ up to 90.06%. In addition, the presence of carbonate mineralizing bacteria can increase montmorillonite’s desorption rate to over 81%, greatly enhancing its capacity for reuse. Therefore, our research work contributes to expanding the potential of montmorillonite and carbonate mineralizing bacteria in the treatment of heavy metal-polluted waters.