Diffusion of native defects such as vacancies and their interactions with impurities are fundamental to semiconductor crystal growth, device processing, and design. However, the transient equilibration of native defects is difficult to directly measure. We used (AlxGa1−x)2O3/Ga2O3 superlattices (SLs) to detect and analyze transient diffusion of cation vacancies during annealing in O2 at 1000–1100 °C. Using a novel finite difference scheme for diffusion with time- and space-varying diffusion constants, we determined diffusion constants for Al, Fe, and cation vacancies, including the vacancy concentration dependence for Al. In the case of SLs grown on Sn-doped β-Ga2O3 (010) substrates, gradients observed in the extent of Al diffusion indicate a supersaturation of vacancies in the substrates that transiently diffuse through the SLs coupled strongly to Sn and thus slowed compared to undoped cases. In the case of SLs grown on (010) Fe-doped substrates, the Al diffusion is uniform through the SLs, indicating a depth-uniform concentration of vacancies. We find no evidence for the introduction of VGa from the free surface at rates sufficient to affect Al diffusion at at. % concentrations, establishing an upper bound on surface injection. In addition, we show that unintentional impurities in Sn-doped Ga2O3 such as Fe, Ni, Mn, Cu, and Li also diffuse toward the surface and accumulate. Many of these likely have fast interstitial diffusion modes capable of destabilizing devices, thus suggesting that impurities may require further reduction. This work provides a method to measure transients in diffusion-mediating native defects otherwise hidden in common processes such as ion implantation, etching, and film growth.