The impact of chlorine and UV on the induction of VBNC state in two faecal indicator bacteria (Escherichia coli and Enterococcus faecium) and their subsequent resuscitation was investigated in this study. Results showed that over half of the bacterial populations in the effluents remained viable despite the complete loss of culturability after chlorine or UV treatment. Resuscitation of VBNC cells was observed in nutrient-rich conditions after the cessation of treatment. Both VBNC and resuscitated cells exhibited substantial differences in their gene expression profiles when compared to the untreated cells. The UV- and chlorine-induced VBNC cells appeared to have different preferences in regulating the expression of functional genes. This study provided insights into the stress tolerance and the alterations of metabolic activities of VBNC and resuscitated bacteria in sewage induced by the chlorine and UV disinfection processes.