The transition towards a new risk approach for the Dutch national safety assessment of primary flood defences has been taken as an opportunity to improve the dealings with uncertainties. The probabilistic models for the new safety assessment (WBI2017) not only deal with the natural variability, but also with so-called epistemological uncertainties. One class of epistemological uncertainties is the model uncertainty in the hydrodynamic models used. The quantification of the water level uncertainty depends on the dominant hydraulic processes in each water system and is chosen to be independent of the return period. However, water level frequency lines derived including model uncertainty sometimes conflict with the physics. A comparative analysis is carried out to assess the performance of Hydra-NL w.r.t. observations and to analyse if physical processes that play an important role in each fresh water system are represented correctly after the inclusion of model uncertainty with the WBI2017 method. This study showed that the estimated exceedance probability of actual water levels in the tidal river area and lake area are often overestimated by the Hydra-model even without model uncertainty. When model uncertainties are included the overestimations become even larger. Furthermore, the inclusion of model uncertainty sometimes gives an incorrect representation of the underlying physical processes. The effect of the model uncertainty gets larger when the water level frequency line becomes flatter. This is e.g. the case at locations where the water levels are influenced by the closure of the Europoortkering and upstream of the flood channel near Veessen-Wapenveld. It can be argued that water level uncertainties are likely to decrease in these situations, because a reservoir is more predictable than a flowing river and the operation of the flood channel results in an enlarged conveyance that is less sensitive than an average river profile. The hypothesis that the inclusion of model uncertainty according to WBI2017 results in an incorrect representation of the underlying physical processes is further analysed for several case studies in the upper river area and the lake area. Varying river schematisations and two river interventions (flood channel and retention area) are modelled to compare the WBI2017 method with a more physics-based approach. In this physics-based approach the hydraulic roughness of the main channel and/or floodplains is incorporated as additional stochastic variable for the derivation of water level frequency lines. It is shown that the water level uncertainty becomes smaller for wide rivers where the water level frequency line becomes flatter. The cases where river interventions are present the water level uncertainty is bounded, because of the environment/geometry that influences the water levels. According to the physics-based method the water level uncertainties are location and discharge dependent, which are both not integrated in the WBI2017 method. For the lake area the focus is on locations where high water levels are predominantly determined by the wind that is causing a set-up on the lake. By considering an empirical parameter of the "capped Wu" formula as additional stochastic variable the uncertainty of the drag coefficient is modelled for the physics-based method. The physics-based method demonstrates that the water level uncertainty is larger for higher decimate heights and vice versa. It can be concluded that it is not valid to choose one uniform standard deviation of the water level for all wind-dominated locations, as it is done for WBI2017. It is recommended to include the model uncertainty by considering a model parameter in the hydrodynamic model for the upper river area and lake area as additional stochastic variable in the Hydra-models, to model uncertainty in the water level. In other water systems it becomes more complex, because several equally important sources of uncertainty are present. Still, the most important model uncertainty sources could considered stochastically, but computational effort would become the limiting factor