Si nanocrystals embedded in thermally grown SiO2 have been annealed at temperatures between 400 and 900 degreesC in a variety of atmospheres. Positron annihilation spectroscopy has been employed to study changes in the interface regions between nanocrystalline Si (nc-Si) and SiO2 with the support of photoluminescence measurements. We find that nitrogen and oxygen are trapped in the voids around nc-Si at low annealing temperatures. High-temperature annealing during the formation of nc-Si causes hydrogen originally residing in the SiO2/substrate region to enter the SiO2 structure. Hydrogen diffuse back to the SiO2/substrate region on annealing in vacuum at 400 degreesC because no other impurities block its diffusion channels. At annealing temperatures above 700 degreesC, both nitrogen and oxygen react with nc-Si, resulting in a volume increase. This introduces stress in the SiO2 matrix, which is relaxed by the shrinkage of its intrinsic open volume. The present data suggest that nitrogen suppresses Si diffusion in SiO2, so that the agglomeration of nc-Si is slower during annealing in nitrogen than in oxygen or vacuum.