Disease outbreaks related to drinking water significantly decreased due to advances in drinking water treatment, especially water disinfection. However, the build-up of pathogen tolerance and resistance against widely used disinfectants in drinking water treatment and potable water reuse is a concern that needs to be understood and managed. Therefore, there is a need to improve both pathogen inactivation during disinfection and our understanding of factors that could contribute to pathogen resistance against disinfectants. This dissertation’s overarching goal was two-fold: 1) improve our understanding of bacterial responses to disinfectants, and 2) investigate the development of bacterial tolerance and resistance against disinfectants. The biological responses of Escherichia coli at the physiological and molecular levels to two different disinfectants, ferrate and monochloramine, were investigated. Overall, ferrate’s faster disinfection kinetics (by 2.8 times) compared to monochloramine influenced E. coli’s inactivation mechanisms, physiological responses, and resistance development. Disinfectant reactivity also influenced resistance development against repeated ferrate and monochloramine disinfection. E. coli cultures repeatedly disinfected with monochloramine developed resistance after 12+ treatment rounds, whereas cells repeatedly exposed to ferrate did not. Furthermore, monochloramine induced the formation of highly tolerant phenotypic variants, known as persisters, in approximately 100% of the residual culturable population. In contrast, ferrate disinfection triggered the formation of a significantly smaller percentage of persister cells. Like VBNC cells, persisters develop due to stressors; however, they do not fall into deep dormancy levels. Therefore, the formation of persister and VBNC subpopulations following monochloramine suggests that monochloramine induced metabolic heterogeneity, leading to different cell-to-cell dormancy levels. In summary, this dissertation highlights important findings on the formation of highly tolerant and resistant sub-populations in response to disinfectants. The prevalence of VBNC, persister, and disinfectant-resistant cells in the finished water microbiome could negatively impact potable water quality and its biological stability. Future advanced water treatment trains may need to consider the formation of VBNC, persister and resistant pathogens and implement measures that effectively eradicate them. The improved understanding of factors or treatment conditions that lead to the occurrence of tolerant and resistant bacteria during potable water reuse could help inform and strengthen future health risk assessments.