Design guideline safety factors (SF) are based on the accumulated experience of the industry and account for the uncertainty and variability inherent in the wastewater treatment process. Models on the other hand, as implemented in most commercial simulators, do not explicitly account for uncertainty. This paper discusses how to deal with variability and uncertainty in an explicit way when using a dynamic model combined with uncertainty analysis to perform a post-project evaluation. Through the use of time series, the response of the design to the variability of key inputs can be captured in the dynamic model. In order to incorporate uncertainty, selected model parameters can be described with probability density functions (PDF). Scenario analysis can be used to simulate discreet operational conditions or events. Uncertainty can then be propagated to the dynamic model outputs with the use of Monte Carlo simulations. To test this approach, the upgrade of the Eindhoven WWTP (Waterboard De Dommel, The Netherlands) was selected as a case study. The project focused on how variability and uncertainty are incorporated in design guidelines and highlighted key issues linked to the inclusion of the sources of uncertainty in the calibrated model.