Predicting the disinfection performance of a full-scale reactor in drinking water treatment is associated with considerable uncertainty. In view of quantitative risk analysis, this study assesses the uncertainty involved in predicting inactivation of Cryptosporidium parvum oocysts for an ozone reactor treating lake water. A micromodel is suggested which quantifies inactivation by stochastic sampling from density distributions of ozone exposure and lethal ozone dose. The ozone exposure distribution is computed with a tank in series model that is derived from tracer data and measurements of flow, ozone concentration and ozone decay. The distribution of lethal ozone doses is computed with a delayed Chick–Watson model which was calibrated by Sivaganesan and Marinas [2005. Development of a Ct equation taking into consideration the effect of Lot variability on the inactivation of Cryptosporidium parvum oocysts with ozone. Water Res. 39(11), 2429–2437] utilizing a large number of inactivation studies. Parameter uncertainty is propagated with Monte Carlo simulation and the probability of attaining given inactivation levels is assessed. Regional sensitivity analysis based on variance decomposition ranks the influence of parameters in determining the variance of the model result. The lethal dose model turns out to be responsible for over 90% of the output variance. The entire analysis is re-run for three exemplary scenarios to assess the robustness of the results in view of changing inputs, differing operational parameters or revised assumptions about the appropriate model. We argue that the suggested micromodel is a versatile approach for characterization of disinfection reactors. The scheme developed for uncertainty assessment is optimal for model diagnostics and effectively supports the management of uncertainty.