This study provides an in-depth geophysical interpretation of the geology of the Stanthorpe region with a particular focus on hydrothermal alteration. The radiometric ternary map outlines the main lithological divisions in the region, which together with Th and Th/K ratio maps distinguish various granitic suites. Magnetic signatures delineate a non-magnetic zone within the low to moderately magnetic Stanthorpe Granite. The non-magnetic section, a north–northwest trending belt with a high density of faults and dykes is interpreted as a hydrothermal alteration zone that is narrower in the north, widens southwards, and is much more extensive at depth than is suggested by the surface alteration pattern. Modelling of gravity data reveals a massive low-density granitic intrusion extending to a depth of 10–15 km. The low-gravity section with modelled rock densities between 2450 and 2670 kg/m3 coincides with the low magnetic susceptibility zone in the magnetic model. High K, low Th and low Th/K also characterise the sections of the Stanthorpe Granite that have both low gravity and magnetic responses. Also conspicuous in the geophysical signatures within the non-magnetic zone is an ovoid feature of low magnetic response, high uranium content with moderate density, interpreted as a granitic pluton. Thus, decrease in magnetisation, changes in K concentration and corresponding low gravity with an associated high density of faults, fractures and dykes in the Stanthorpe region are the main features of the quartz–sericite–chlorite–muscovite hydrothermal alteration.