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 Pontederia crassipes (a widespread hydrophyte in the karst area) from karst water. The Pb concentration, Pontederia crassipes 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.