Abstract. Uncertainty of groundwater model predictions has in the past mostly been related to uncertainty in the hydraulic parameters, whereas uncertainty in the geological structure has not been considered to the same extent. Recent developments in theoretical methods for quantifying geological uncertainty have made it possible to consider this factor in groundwater modeling. In this study we have applied the multiple-point geostatistical method (MPS) integrated in the Stanford Geostatistical Modeling Software (SGeMS) for exploring the impact of geological uncertainty on groundwater flow patterns for a site in Denmark. Realizations from the geostatistical model were used as input to a groundwater model developed from Modular three-dimensional finite-difference ground-water model (MODFLOW) within the Groundwater Modeling System (GMS) modeling environment. The uncertainty analysis was carried out in three scenarios involving simulation of groundwater head distribution and travel time. The first scenario implied 100 stochastic geological models all assigning the same hydraulic parameters for the same geological units. In the second scenario the same 100 geological models were subjected to model optimization, where the hydraulic parameters for each of them were estimated by calibration against observations of hydraulic head and stream discharge. In the third scenario each geological model was run with 216 randomized sets of parameters. The analysis documented that the uncertainty on the conceptual geological model was as significant as the uncertainty related to the embedded hydraulic parameters.