Heavy metal contamination has long been a tough challenge. Recently, enzyme-induced carbonate precipitation (EICP) has been proposed to handle this problem. This paper aims to explore the efficacy, process, and mechanisms of EICP using crude sword bean urease extracts to remediate Zn²⁺, Ni²⁺, and Cr(VI) contamination. A series of liquid batch tests and geochemical simulations, as well as microscopic analyses, were conducted. The liquid batch test results show that Zn²⁺, Ni²⁺, and Cr(VI) can be effectively immobilized by the EICP method, and the highest immobilization percentage was observed for Zn²⁺, reaching up to 99%. Ni²⁺ and Cr(VI) were immobilized at 62.4% and 24.4%, respectively. Additionally, the immobilization percentage of heavy metals increased with the concentration of added Ca²⁺. The simulation results and XRD results reveal that the organic molecules in crude sword bean urease can promote ZnCO₃, Zn(OH)₂, Zn₅(CO₃)₂(OH)₆, and NiCO₃ precipitation. The FTIR and SEM-EDS results provide evidence for heavy metal adsorption by the functional groups in crude urease and calcium carbonate. The liquid batch test results, as well as the simulation results and the microscopic analysis results, indicate that the mechanism of EICP in heavy metal remediation can be summarized as biomineralization to form heavy metal carbonate precipitates and metal hydroxide precipitates, adsorption by calcium carbonate, and adsorption or complexation or promoting nucleation by organic molecules.