Many 3D hydrostratigraphic models of the subsurface are interpreted as deterministic models, where an experienced modeler combines relevant geophysical and geological information with background geological knowledge. Depending on the quality of the information from the input data, the interpretation phase will typically be accompanied by an estimated qualitative interpretation uncertainty. Given the qualitative nature of uncertainty, it is difficult to propagate the uncertainty to groundwater models. In this study, a stochastic-simulation-based methodology to characterize interpretation uncertainty within a manual-interpretation-based layer model is applied in a groundwater modeling setting. Three scenarios with different levels of interpretation uncertainty are generated, and three locations representing different geological structures are analyzed in the models. The impact of interpretation uncertainty on predictions of capture zone area and median travel time is compared to the impact of parameter uncertainty in the groundwater model. The main result is that in areas with thick and large aquifers and low geological uncertainty, the impact of interpretation uncertainty is negligible compared to the hydrogeological parameterization, while it may introduce a significant contribution in areas with thinner and smaller aquifers with high geologic uncertainty. The influence of the interpretation uncertainties is thus dependent on the geological setting as well as the confidence of the interpreter. In areas with thick aquifers, this study confirms existing evidence that if the conceptual model is well defined, interpretation uncertainties within the conceptual model have limited impact on groundwater model predictions.