Polypyrrole (PPy) films modified with copper species were used for disinfection of well water contaminated with Escherichia coli (E. coli). For that purpose a laboratory-scale continuous flow system with a parallel plate flow chamber configuration was implemented operating under laminar flow. Three flow rates were considered. The testing conditions did not affect the morphology of the modified PPy films, even after 5 h of continuous use at the largest flow rate examined. The results show that the bacteria killing process can be described by a first-order kinetic law at all Reynolds numbers. As the flow rate increases, the concentration of Cu species released from the electrodes enhances, accelerating the disinfection process. Re-inoculation and Cu-recharging tests showed bactericidal effects very similar to those displayed by the freshly prepared electrodes. It is concluded that PPy/Cu-modified electrodes installed in the laboratory-scale continuous flow system are effective for the water disinfection process.