We demonstrate the application of proton transfer time-of-flight mass spectrometry (PTR-TOF-MS) in monitoring the kinetics of disinfectant decay in water with a sensitivity one to three orders of magnitude greater than other analytical methods. Chemical disinfection inactivates pathogens during water treatment and prevents regrowth as water is conveyed in distribution system pipes, but it also causes formation of toxic disinfection by-products. Analytical limits have hindered kinetic models, which aid in ensuring water quality and protecting public health by predicting disinfection by-products formation. PTR-TOF-MS, designed for measuring gas phase concentrations of organic compounds, was able to simultaneously monitor aqueous concentrations of five inorganic haloamines relevant to chloramine disinfection under drinking water relevant concentrations. This novel application to aqueous analytes opens a new range of applications for PTR-TOF-MS.