Effective porosity plays an important role in contaminant management. However, the effective porosity is often assumed to be constant in space and hence heterogeneity is either neglected or simplified in transport model calibration. Based on a calibrated highly parametrized flow model, a three-dimensional advective transport model (MODPATH) of a 1300 km2 coastal area of southern Denmark and northern Germany is presented. A detailed voxel model represents the highly heterogeneous geological composition of the area. Inverse modelling of advective transport is used to estimate the effective porosity of 7 spatially distributed units based on apparent groundwater ages inferred from 11 14C measurements in Pleistocene and Miocene aquifers, corrected for the effects of diffusion and geochemical reactions. By calibration of the seven effective porosity units, the match between the observed and simulated ages is improved significantly, resulting in a reduction of ME of 99 % and RMS of 82 % compared to a uniform porosity approach. Groundwater ages range from a few hundred years in the Pleistocene to several thousand years in Miocene aquifers. The advective age distributions derived from particle tracking at each sampling well show unimodal (for younger ages) to multimodal (for older ages) shapes and thus reflect the heterogeneity that particles encounter along their travel path. The estimated effective porosity field, with values ranging between 4.3 % in clay and 45 % in sand formations, is used in a direct simulation of distributed mean groundwater ages. Although the absolute ages are affected by various uncertainties, a unique insight into the complex three-dimensional age distribution pattern and potential advance of young contaminated groundwater in the investigated regional aquifer system is provided, highlighting the importance of estimating effective porosity in groundwater transport modelling and the implications for groundwater quantity and quality assessment and management.