We have used low-energy electron-excited nanoscale-luminescence (LEEN) spectroscopy combined with ultrahigh vacuum (UHV) surface science techniques to probe deep level defect states at GaN free surfaces, metal-GaN contacts and GaN/InGaN quantum well interfaces. Employing energies as low as 100 eV and ranging up to 5 keV, we have been able to establish the local nature of these states and their spatial variation normal to the interface plane on an incremental 10-20 nm scale. Coupled with surface science techniques, these measurements show that a variety of discrete deep levels form deep within the GaN band gap due to (a) native defects, (b) metal-induced bonding, (c) reaction products, and (d), in the case of GaN/InGaN heterostructures, local interface phase changes. These results suggest that deep levels are a common feature at GaN interfaces and hence can play an integral role in charge transfer and the formation of local dipoles at GaN heterostructures.