The aim of this work was to investigate the effectiveness of a high voltage multi-spark electric discharge, with pulse energy of 1 Joule, in killing microorganisms in wastewater. Wastewater from primary treated effluent arising from domestic and industrial sources was abstracted for continuous pulsed discharge disinfection. The wastewater contained a large mixed population of microorganisms (∼107 CFU ml−1 [109 CFU 100 ml−1] total aerobic heterotrophic bacteria) including vegetative cells and spores. The electrical conductivity of the wastewater ranged from 900–1400 μS cm−1 and it was shown that a specific energy of 1.25–1.5 J cm−3 was required to achieve 1 log reduction in bacterial (faecal coliforms/total aerobic heterotrophs) content. This is higher than that previously shown to reduce the population of E. coli in tap water of low conductivity, demonstrating the role of total wastewater constituents, including dissolved and particulate substances, water colour and the presence of microbial spores, in effective disinfection. The system can be engineered to eradicate microbial populations to levels governed by legislation by increasing treatment time or energy input.