Heavy metals (HMs) are toxic elements which contaminate the water bodies in developing countries because of their excessive discharge from industrial zones. Rice (Oryza sativa L) crops are submerged for a longer period of time in water, so irrigation with HMs polluted water possesses toxic effects on plant growth. This study was initiated to observe the synergistic effect of bacteria (Bacillus cereus and Lysinibacillus macroides) and zinc oxide nanoparticles (ZnO NPs) (5, 10, 15, 20 and 25 mg/L) on the rice that were grown in HMs contaminated water. Current findings have revealed that bacteria, along with ZnO NPs at lower concentration, showed maximum removal of HMs from polluted water at pH 8 (90 min) as compared with higher concentrations. Seeds primed with bacteria grown in HM polluted water containing ZnO NPs (5 mg/L) showed reduced uptake of HMs in root, shoot and leaf, thus resulting in increased plant growth. Furthermore, their combined effects also reduced the bioaccumulation index and metallothionine (MTs) content and enhanced the tolerance index of plants. This study suggested that synergistic treatment of bacteria with lower concentrations of ZnO NPs helped plants to reduce heavy metal toxicity, especially Pb and Cu, and enhanced plant growth.