We present a systematic study of the impact of layer structure design on the channel temperature of AlGaN/GaN high electron mobility transistor (HEMT) structures. Device layer structures have been optimized to obtain minimum overheating temperature at high dissipated power in channel of HEMTs grown on different substrates. It is shown that temperature increase has opposite dependence on buffer thickness for sapphire and SiC substrates. Noise spectroscopy is also used to monitor the self-heating effect. Moreover, it is shown that the room temperature spectra can be used to determine the activation energy of the traps. An irreversible improvement in mobility is registered after irradiation of AlGaN/GaN heterostructures at a total dose 1x10⁶ rad of ⁶⁰Co gamma rays.