Heavy metal contamination is widespread in the environment and has resulted in numerous adverse consequences for the ecosystem. Ureolytic microorganisms are known to immobilize heavy metals by co-precipitation with calcium carbonates, which are formed during microbial hydrolysis of urea. In this work, we described a novel halophilic ureolytic bacterium (Exiguobacterium sp. JBHLT-3) and examined the relationship between ureolytic-driven mineralization of CaCO3 and heavy metal mitigation. The growth of strain JBHLT-3 occurred at salinities between 3 and 12% with an optimum at 6%. This strain was capable of precipitating calcite and vaterite under non-growth conditions. Lead (Pb) was selected as a model heavy metal for this study and amended into the bio-precipitation systems at a starting concentration of 1 mM. The strain JBHLT-3 efficiently removed Pb from saline solutions via incorporation within microbially-induced calcium carbonates. Mineralogical analysis showed that calcite had higher uptake of Pb2+ than vaterite. The increasing solution salinity progressively increased the vaterite fraction in the bio-precipitates but reduced the removal efficiency of Pb2+. Nevertheless, the removal efficiency could be still as high as 89% in the cultures incubated in a 12% salinity medium. Our results highlight the positive role of halophilic ureolytic microbes in remediating heavy metal-contaminated saline environments. Display omitted •A novel halophilic ureolytic bacterium, Exiguobacterium sp. JBHLT-3, has the capacity to induce CaCO3 precipitation.•Removal of Pb2+ from saline solutions is initiated by microbially-induced carbonation.•Calcite has higher uptake of Pb2+ than vaterite.•Solution salinity reduces the removal efficiency of Pb2+.