To investigate the thermal structure of central Te Riu a Māui/Zealandia continent we estimate the depth to base of magnetic sources (DBMS), using an updated compilation of magnetic data. We calculate thousands of power spectral density estimates and solve an analytic solution for the fractal distribution of magnetization using a Bayesian method constrained by a sediment thickness model. Our DBMS results are broadly similar to a global model yet show complex relationships with independent models of crust and elastic thicknesses, and depth to base of seismicity (D90). Across central Zealandia, DBMS occurs above, coincident with, and below the Moho reflecting that factors additional to temperature influence DBMS. Away from subduction zones crustal thickness likely modulates DBMS while plate margins show varying influence dependent on margin characteristics. In the Taupō Volcanic Zone we interpret DBMS to reflect Curie point temperature at an average depth of 9–11 km. Error analysis shows that the choice of prior influences the posterior standard deviation and can result in counter intuitive error versus DBMS relationships. We use the DBMS as a basal temperature isotherm in heat flow models to compare with heat flow derived from borehole temperature measurements. Using the standard Curie point temperature of 580°C we find that DBMS derived heat flow models over estimate heat flow in areas underlain by plutonic rocks. We propose this reflects a higher titanomagnetite content in these rocks, although detailed studies of the magnetic mineralogy of Zealandia's plutonic rocks are required.