The effects of root exudate addition on Fe(II) oxidation, nitrate degradation, and heavy metal removal by Clostridium sp. strain PXL2 were studied. The root exudate addition could increase the average oxidation rate of Fe(II) from 0.52 to 0.68 mM Fe(II)/d. The removal rate of nitrate, arsenic, and mercury could be increased from 54% to 95%, 84% to 99%, and 60% to 86%, respectively. The complexation of Fe(III) with the root exudates was analyzed by quenching titration. The results showed that there was a complexation of root exudates with Fe(III). This complexation resulted in increased precipitation of iron oxides and further promoted the removal of heavy metals.