A growing number of fluorescent stains and probes are available that allow in situ, intracellular assessment of various aspects of bacterial physiology at the level of the individual cell. In this study, a suite of these stains and probes were used in conjunction with viable plate counts to assess the effect of chlorine disinfection on membrane potential [Rh123 and DiBAC4(3)], membrane integrity (LIVE/DEAD BacLight kit), respiratory activity (CTC), microcolony formation (MicroStar J system), esterase activity (ScanRDI J system), substrate responsiveness (DVC) and disinfection resistance in the commensal pathogen E.coli O157:H7. After 14 days of starvation, DVC values slightly decreased while all other assays remained relatively constant and equivalent. Chlorine resistance progressively increased through the starvation period. By 29 days, there was no significant difference between control cultures and those that had been treated with chlorine (0.5 mg/L). In situ assessment of physiological activity by examining multiple targets, as demonstrated in this study, permits a more comprehensive determination of the site and extent of injury in bacterial cells following sublethal disinfection. These in situ techniques allow the assessment of chlorine induced injury by providing information on altered bacterial physiology and support their application in rapid methods for detecting stressed bacteria.