In this work, we fabricate Van der Pauw structures on AlGaN/GaN high electron mobility transistors (HEMTs) with both SiN and AlN passivation layers and both SiC and GaN substrates to study temperature dependent electron transport properties of 2 dimensional electron gases (2DEG) in as-fabricated and proton irradiated devices. We confirm that using a GaN substrate or AlN passivation layer enhances the mobility particularly at low temperatures, though this enhancement is greatly reduced upon irradiating the samples with high proton fluences. Our results suggest that the sheet density may be affected by Al diffusion in the sample creating electron donating impurities, which freeze out around 200 K and are more prominent in AlN passivated samples and minimized by using a GaN over a SiC substrate. Additionally, we show that a large dose of radiation forms traps in the AlGaN layer, which drop the sheet density at high proton fluences. GaN, among other wide bandgap semiconductors, is of considerable interest for next-generation energy efficient, high performance devices because their high electron mobility and high breakdown voltage allows them to operate at higher voltages, frequencies, and temperatures than current Si-or GaAs-based devices. One application is the production of AlGaN/GaN high electron mobility transistors (HEMTs) for microwave power amplifiers, making the study of these devices robustness in high energy proton radiation important for potential space applications.