The thermal structure of sedimentary basins is largely dependent on complex three-dimensional effects encompassing architecture, geology and groundwater, making it difficult to describe in a one-dimensional model. New equilibrated down-hole temperature measurements in the Sydney Basin, in conjunction with regional scale thermal modelling using the geodynamics simulation software Underworld, can provide an accurate assessment of the thermal structure of the basin. When compared with extrapolation maps, these results highlight important limitations of utilising extrapolation maps as an unaccompanied geothermal exploration tool. The extrapolated temperature method creates a 'temperature-at-depth' map, which propagates and exaggerates near surface variations, and is limited by coverage and number of boreholes that have temperature measurements recorded. Numerical simulations of basin heat flow, using basic material properties, combined with a deep three-dimensional geological model and calibrated by measured equilibrated temperature data are not limited by the borehole coverage but rather the chosen resolution of the model. The Underworld thermal model provides a realistic estimation of temperature at depth within the Sydney Basin, a clearer understanding of thermal structure and allows a more comprehensive assessment of potential geothermal targets.