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Bicarbonate ions (HCO₃⁻) are abundant in karst water with poor lead (Pb) utilization and biodegradation. This study aimed to investigate the mechanism of HCO₃⁻ on the Pb removal efficiency and uptake ability of <i>Pontederia crassipes</i> (a widespread hydrophyte in the karst area) from karst water. The Pb concentration, <i>Pontederia crassipes</i> morphology, and functional group were detected. As the HCO₃⁻ molarity in karst water increased (3, 4, and 5 mmol/L), the removal of Pb increased (85.31%, 93.28%, and 95.16%), whereas the bioconcentration amount of Pb decreased (573, 501, and 301 mg/kg), mainly due to the insoluble PbCO₃ and Pb (OH)₂. The Pb bioconcentration factor was the highest (15,564) at 4 mmol/L HCO₃⁻ due to the maximum strength of cation exchange and cell wall protein C=O. High HCO₃⁻ molarities changed the variety of positive ions of cation exchange (HCO₃⁻ ≤ 4 mmol/L: Na, K, and Mg; HCO₃⁻ > 4 mmol/L: Mg and K), and relieved the breaking of roots, stomatal closure, and vascular system shrinking. Moreover, high HCO₃⁻ molarities diminished the C≡C oxidation, enlarged the displacement of SO₄²⁻ and C-O, and stimulated the methyl transfer reaction and the bonding between -CH₃ and Pb.