Reliable groundwater model predictions are dependent on representative models of the geological environment, which can be modelled using several different techniques. In order to inform the choice of the geological modelling technique, the differences between a layer modelling approach and a voxel modelling approach were analyzed. The layer model consist of stratigraphically ordered surfaces, while the voxel model consist of a structured mesh of volumetric pixels. Groundwater models based on the two models were developed to investigate their impact on groundwater model predictions. The study was conducted in the relatively data-dense area Egebjerg, Denmark, where both a layer model and a voxel model has been developed based on the same data and geological conceptualization. The characteristics of the two methodologies for developing the geological models were shown to have a direct impact on the resulting models. The differences between the layer and the voxel models were however shown to be diverse and not related to larger conceptual elements with few exceptions. The analysis showed that the geological modelling approaches had an influence on preferred parameter values and thereby groundwater model predictions of hydraulic head, groundwater budget terms and particle tracking results. A significance test taking into account the predictive distributions showed that for many predictions the differences between the models were significant. The results suggest that the geological modelling strategy has an influence on groundwater model predictions even if based on the same geological conceptualization.