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Wastewater disinfection processes are typically designed according to heuristics derived from batch experiments in which the interaction among wastewater quality, reactor hydraulics, and inactivation kinetics is often neglected. In this paper, a computational fluid dynamics (CFD) study was conducted in a nondeterministic (ND) modeling framework to predict the Escherichia coli inactivation by peracetic acid (PAA) in municipal contact tanks fed by secondary settled wastewater effluent. The extent and variability associated with the observed inactivation kinetics were both satisfactorily predicted by the stochastic inactivation model at a 95% confidence level. Moreover, it was found that (a) the process variability induced by reactor hydraulics is negligible when compared to the one caused by inactivation kinetics, (b) the PAA dose required for meeting regulations is dictated equally by the fixed limit of the microbial concentration as well as its probability of occurrence, and (c) neglecting the probability of occurrence during process sizing could lead to an underestimation of the PAA dose required by as much as 100%. Finally, the ND-CFD model was used to generate sizing information in the form of probabilistic disinfection curves relating E. coli inactivation and probability of occurrence with the average PAA dose and PAA residual concentration at the outlet of the contact tank.