Sedimentological processes often result in complex three-dimensional subsurface heterogeneity of hydrogeological parameter values. Variogram-based stochastic approaches are often not able to describe heterogeneity in such complex geological environments. This work shows how multiple-point geostatistics can be applied in a realistic hydrogeological application to determine the impact of complex geological heterogeneity on groundwater flow and transport. The approach is applied to a real aquifer in Belgium that exhibits a complex sedimentary heterogeneity and anisotropy. A training image is constructed based on geological and hydrogeological field data. Multiple-point statistics are borrowed from this training image to simulate hydrofacies occurrence, while intrafacies permeability variability is simulated using conventional variogram-based geostatistical methods. The simulated hydraulic conductivity realizations are used as input to a groundwater flow and transport model to investigate the effect of small-scale sedimentary heterogeneity on contaminant plume migration. Results show that small-scale sedimentary heterogeneity has a significant effect on contaminant transport in the studied aquifer. The uncertainty on the spatial facies distribution and intrafacies hydraulic conductivity distribution results in a significant uncertainty on the calculated concentration distribution. Comparison with standard variogram-based techniques shows that multiple-point geostatistics allow better reproduction of irregularly shaped low-permeability clay drapes that influence solute transport.