Heteroepitaxial GaN-based devices have transformed electronic and optoelectronic applications, although the potentially significant effective boundary resistance (TBReff), which exists between the GaN layer and substrate (e.g. SiC, Si, diamond), can poses major heat transport bottleneck. It would be advantageous to be able to measure the TBReff of bare wafers non-destructively, enabling wafer mapping for defect screening before device fabrication, or the reduction of TBReff through growth parameter tuning, although this has not been possible using conventional techniques. A method has recently been developed for performing transient thermoreflectance (TTR) measurements without modifying the surface of GaN wafers: Above-bandgap pump and probe lasers are used to heat and monitor the GaN surface temperature directly; the latter exploits the temperature dependent Fresnel reflection (refractive index contrast). We demonstrate that this generic TTR technique can be applied to thermal resistance measurements of GaN layers on various substrates, including SiC, Si and diamond, over a range of ambient temperatures.