Pure water is the fundamental requisite for human life. The water has been recycled naturally but not in an adequate amount for consumption. Nanotechnology with extraordinary applications provides competent ways for the decontamination of contaminated water. In the present study MnWO4 nanoflowers endorsed with inherent antibacterial activity were successfully synthesized by facile hydrothermal approach. XRD, SEM, EDX spectroscopy and UVDRS were used to characterize the as-synthesized nanoflowers. Gram negative Escherichia coli ATCC 52922 bacterium was used as model organism to test antibacterial activity of as-synthesized MnWO4 nanoflowers. This study was conducted to optimize minimum concentration of MnWO4 nanoflowers and maximum contact time required to achieve complete inactivation of bacteria present in contaminated water. Minimum inhibitory concentration (MIC) of MnWO4 nanoflowers was found to be 10 μg/ml. The assessment and interpretation of bacterial viability was done using dual fluorescent staining. The synthesized 3D-nanoflowers were found as potent bactericides. Thus, MnWO4 nanoflowers emerged to be very good future material for disinfection of biological pollutants present in the contaminated water reservoirs and as an anti-biofouling agent.