Using enriched isotopes, we developed a method to elucidate the long-standing issue of Ge transport governing the strain-driven self-assembly. Here 76Ge was employed to form the 2D metastable layer on a Si(001) surface, while the 3D transition and growth were completed by additional evaporation of 70Ge. This isotope tracing combined with the analysis of the Ge-Ge LO phonon enables the tracking of the origin of Ge atoms and their flow towards the growing islands. This atomic transport was quantified based on the quasiharmonic approximation of Ge-Ge vibrations and described using a rate equation model.