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Removal of calcium and magnesium ions through biomineralization induced by bacteria has been proven to be an effective and environmentally friendly method to improve water quality, but the process and mechanism are far from fully understood. In this study, a newly isolated probiotic <i>Bacillus licheniformis</i> SRB2 (GenBank: KM884945.1) was used to induce the bio-precipitation of calcium and magnesium at various Mg/Ca molar ratios (0, 6, 8, 10, and 12) in medium with 30 g L^&#8722;1 sodium chloride. Due to the increasing pH and HCO₃^&#8722; and CO₃^2&#8722; concentrations caused by NH₃ and carbonic anhydrase, about 98% Ca²⁺ and 50% Mg²⁺ were precipitated in 12 days. The pathways of bio-precipitation include extracellular and intracellular processes. Biominerals with more negative &#948;¹³C values (&#8722;16&#8241; to &#8722;18&#8241;) were formed including calcite, vaterite, monohydrocalcite, and nesquehonite with preferred orientation. The nucleation on extracellular polymeric substances was controlled by the negatively charged amino acids and organic functional groups. The intracellular amorphous inclusions containing calcium and magnesium also contributed to the bio-precipitation. This study reveals the process and mechanism of microbial desalination for the removal of calcium and magnesium, and provides some references to explain the formation of the nesquehonite and other carbonate minerals in a natural and ancient earth surface environment.