A detailed deep 3D geological model is an important basis for many types of exploration and resource modelling. Renewed interest in the structure of the Sydney Basin, driven primarily by sequestration studies, geothermal studies and coal seam gas exploration, has highlighted the need for a model of deep basin geology, structure and thermal state. Here, we combine gravity modelling, seismic reflection surveys, borehole drilling results and other relevant information to develop a deep 3D geological model of the Sydney Basin. The structure of the Sydney Basin is characteristic of a typical intracontinental rift basin, with a deep north-south orientated channel in the Lachlan Fold Belt basement, filled with up to 4 km of rift volcanics, and overlain with Permo-Triassic sediments up to 4 km thick. The deep regional architecture presented in this study will form the framework for more detailed geological, hydrological and geothermal models.