Sewage treatment is crucial for maintaining a sustainable aquatic environment. Before discharge into marine waters, treated effluent undergoes disinfection to reduce microorganisms to acceptable levels. For practicality, the concentration of culturable fecal indicator bacteria (FIB) serves as a proxy to estimate the level of fecal pathogens in the disinfected effluent. UV-C is a commonly used disinfectant that inactivates microbes by damaging their DNA. However, some bacteria can enter a viable but non-culturable (VBNC) state under stress, such as UV treatment. In this state, they remain metabolically active but cannot reproduce and form visible colonies on conventional culture media, leading to an underestimation of FIB concentration and an overestimation of disinfection efficacy. Even worse, VBNC bacteria can resuscitate once stress is removed. Hence, disinfection outcomes cannot be evaluated accurately due to the presence of VBNC cells. Despite the implications of VBNC bacteria for disinfection assessment, little is known about the relationships between the disinfection medium, UV doses, and the prevalence of VBNC E. coli and E. faecium. Therefore, our study conducted microcosm experiments on the UV-C disinfection of these bacterial strains in phosphate-buffered saline (PBS), which served as a baseline, and sterile effluents. The results demonstrated that while UV-C effectively reduced culturable FIB, a significant number of viable cells were still detected in direct viable count assays, indicating a marked increase in VBNC cells. Transcriptomic analyses revealed that varied FIB strains in PBS and sewage exhibit different responses to stress, including changes in metabolic activity and environmental information processing, implying that genetic variations in FIB can carry out distinct approaches to survive. Consequently, culture-based monitoring of disinfection may underestimate the number of viable indicator bacteria and pathogens, leading to a misinterpretation of disinfection efficiency. Poorly disinfected effluents released into marine waters may pose risks to public health and ecosystems. This study underscores the need to optimize disinfection strategies to minimize VBNC cell proportions in effluents and provides insights for improving disinfection practices and the development of new culture media for accurate FIB detection.