Chemical diffusion and interlayer formation in thin layers and at interfaces is of increasing influence in nanoscopic devices, such as nanoelectronics and reflective multilayer optics. Chemical diffusion and agglomeration at interfaces of thin Ru, Mo, Si, and B4C layers have been studied with x-ray photoelectron spectroscopy, cross section electron energy loss spectroscopy, high-angle annular dark field scanning transmission electron microscopy, and energy dispersive x-ray in relation to observations in Ru-on-B4C capped Mo/Si multilayers. Rather than in the midst of the Si layer, silicides and borides are formed at the Si-on-Mo interface front, notably RuSix and MoBx. The interface apparently acts as a precursor for further chemical diffusion and agglomeration of B, Ru, and also other investigated d-metals. Reversed “substrate-on-adlayer” interfaces can yield entirely suppressed reactivity and diffusion, stressing the influence of surface free energy and the supply of atoms to the interface via segregation during thin layer growth.