In this paper, the self assembling properties of taurolipids were used to prepare stable copper nanoparticles (CuNPs), and demonstrated the ability of CuNPs to eradicate the biofilms formed by waterborne pathogens. The synthesized CuNPs display wine red color and exhibited surface plasmon resonance with a maximum at 590 nm. Transmission electron microscopy showed that the CuNPs are well-dispersed with spherical morphology and the size range between 5 and 12 nm. The powder X-ray diffraction study revealed that the CuNPs was free from copper oxide impurities and crystalline with the face centered cubic structure. The CuNPs exhibited excellent anti-biofilm activity against water borne pathogens such as Escherichia coli, Pseudomonas aeruginosa, Salmonella typhi, and Shigella flexneri. Light microscopy and scanning electron microscopy (SEM) study revealed that CuNPs eliminates the mature biofilm at the minimum biofilm eradication concentration of 12.5 μM. The antimicrobial activity of the CuNPs was observed at the minimum inhibitory concentration of 25 μM, indicating the reported CuNPs exhibit true anti-biofilm effect. Fluorescence microscopy and SEM study proved that CuNPs kills the bacteria through membrane damage. The possibility to use CuNPs in cleaning biofilm formed on storage containers was demonstrated through removing the mature biofilm formed on a glass pipe. © 2018 Elsevier Ltd