Mathematical groundwater modelling with homogeneous permeability zones has been used for decades to manage water resources in the Almonte-Marismas aquifer (southwest Spain). This is a highly heterogeneous detrital aquifer which supports valuable ecological systems in the Doñana National Park. The present study demonstrates that it is possible to better characterize this heterogeneity by numerical discretization of the geophysical and lithological data available. We identified six hydrofacies whose spatial characteristics were quantified with indicator variogram modelling. Sequential Indicator Simulation then made it possible to construct a 3D geological model. Finally, this detailed model was included in MODFLOW through the Model Muse interface. This final process is still a challenge due to the difficulty of downscaling to a handy numerical modelling scale. New piezometric surfaces and water budgets were obtained. The classical model with zones and the model with 3D simulation were compared to confirm that, for management purposes, the effort of improving the geological heterogeneities is worthwhile. This paper also highlights the relevance of including subsurface heterogeneities within a real groundwater management model in the present global change scenario.