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[Display omitted] • Nanowire-assisted electroporation (<3.0 V) was the main disinfection mechanism. • DV caused poor cell inactivation on cathode and cell adsorption-fouling on anode. • SWAV enabled effective cell inactivation and fouling resistance on both electrodes. • SWAV showed stable and efficient G- and G + inactivation in DI, tap and lake waters. • SWAV regulated cell migration, adsorption, inactivation, and desorption on nanowire. Nanowire-assisted electroporation is regarded as an effective point-of-use disinfection technique for drinking water, and its performance under direct voltage (DV, U) supply is limited by the poor bacterial inactivation on cathode and bacterial adsorption-fouling on anode. Herein, square-wave alternating voltage (SWAV, ± U) was applied on nanowire electrodes to periodically reverse the cathodic/anodic polarity and their repulsions/attractions with bacterial cells, in turn promoting cell inactivation and fouling resistance. As compared with the gradual decrease in cell inactivation by the biofouling on nanowire anode under DV supply, SWAV supply enabled stable and efficient disinfection with ∼ 2 log higher cell inactivation and ∼ 3 times lower energy consumption (0.32–11.3 Wh/m3/log at 1.0–3.0 V) for various G- (Escherichia coli and Acinetobacter schindleri) and G+ (Enterococcus faecalis and Bacillus cereus) bacteria in deionized water, tap water and lake water. The cell morphology observation, flow cytometry analyses, and quenching experiments of reactive species revealed that electroporation on nanowire interfaces with locally enhanced electric field was the main mechanism for bacterial inactivation under voltages below 3.0 V. It was revealed that reversion of electrophoretic and electrostatic attractions under SWAV supply regulated cell migration, adsorption and desorption on nanowire interface, resulting in cell inactivation and fouling resistance on both nanowire electrodes. This work opens an effective strategy for stable and efficient nanowire-assisted electroporation disinfection. [ABSTRACT FROM AUTHOR]