We compare interfaces of Nb/AlOx-Al/Nb and Nb/ZrOx-Zr/Nb junctions using secondary ion mass spectroscopy and cross-sectional transmission electron microscopy. We have clarified that an interface of the Nb/AlOx-Al/Nb junction is drastically different from that of the Nb/ZrOxZr/Nb junction. An adsorbed water vapor layer plays an important role in suppressing grain boundary diffusion between Nb and Al at the interface of the Nb/AlOxAl/Nb junction. In depositing Nb and Al at low power and cooling the substrate, it is important to control the formation of the adsorbed water vapor layer for fabricating Nb/AlOx-Al/Nb junctions exhibiting excellent current-voltage characteristics.