Characterization of regional aquifer systems has historically been a challenge because of the heterogeneous nature of geology, high costs of gathering high spatial resolution subsurface geological data and large computational processing demands. However, the growing datasets of subsurface properties together with the development of numerical models to further constrain subsurface geology and aquifer characteristics has enabled increasingly accurate representations. In this study, we constructed 3D geological models of six regions of the Great Barrier Reef (GBR) catchment system to identify the type and number of aquifers, evaluate the geometries of the aquifer systems, and to conceptualize groundwater flow directions within the catchment. To do this, we combine surface geology, geological contacts and faults, digital elevation model and drill log data from >49,000 wells. 3D geological models integrated with potentiometric surface maps and faults data revealed that the Wet Tropics, Mackay and Burdekin regions have fractured and porous unconfined aquifer systems, while the Cape York, Fitzroy and Burnett regions have both fractured, porous unconfined and confined aquifers. The size and volume of the aquifers differed due to the differences in geologic histories and ongoing processes. The thickest upper aquifer was identified in the Fitzroy region (average 250 m) followed by Burnett (166 m), while the shallowest upper aquifers exist in the highly deformed regions of the Burdekin (average 67 m) and Mackay (60 m). The orientations of the faults trend in the NW-SE direction and could form conduits for south-easterly groundwater flow as opposed to the predominate easterly flow in the porous unconfined and confined aquifers. The 3D models, aquifer connectivities and geometries can be used as inputs for any local and regional groundwater flow simulations and accurate characterizations of non-point pollution sources in the area. The models also provide crucial information to determine sustainable yields, development potentials, and to evaluate sensitive groundwater areas.