The presence of bacteria and viruses in water has caused many large-scale water disease outbreaks. Cold atmospheric plasma has received much attention as an emerging non-thermal purification technology capable of eliminating micro-organisms, non-ferrous fuels, and heavy metals from water. In this study, a novel gas–liquid diaphragm discharge device that generates air plasma driven by a sinusoidal AC power supply was designed, and its sterilizing effect was investigated. First, the concentrations of reactive oxygen and nitrogen species in the diaphragm discharge were characterized, and the physicochemical properties of activated water were explored. Next, experiments on the inactivation of Pseudomonas aeruginosa were carried out using the device. Finally, pond sewage was treated with the device, and the diversity of micro-organisms in the water was analyzed using 16S rRNA assays to further investigate its applicability. The results showed that the species and quantities of micro-organisms in the water significantly reduced after discharge treatment, with the most significant changes occurring in the Bacillus and Firmicutes species. Thus, this study provides an alternative method for microbial inactivation in sewage treatment.