Understanding the effects of growth conditions on the process of self-organisation of Ge nanostructures on Si is a key requirement for their practical applications. In this study we investigate the effect of preconditioning with a high-temperature hydrogenation step on the nucleation and subsequent temporal evolution of Ge self-assembled islands on Si (001). Two sets of structures, with and without H2 preconditioning, were grown by low pressure chemical vapour deposition (LPCVD) at 650°C. Their structural and compositional evolution was characterised by Rutherford backscattering spectrometry (RBS), atomic force microscopy (AFM) and micro-Raman (μRaman) spectroscopy. In the absence of preconditioning, we observe the known evolution of self-assembled Ge nanostructures on Si (001), from small islands with a narrow size distribution, to a bimodal size distribution, through to large islands. Surface coverage and island size increase steadily as a function of deposition time. On the H2 preconditioned surface, however, both nucleation rates and surface coverage are greatly increased during the early stages of self-assembly. After the first five seconds, the density of the islands is twice that on the unconditioned surface, and the mean island size is also larger, but the subsequent evolution is much slower than in the case of the unconditioned surface. This retardation correlates with a relatively high measured stress within the islands. Our results demonstrate that standard processes used during growth, like H2 preconditioning, can yield dramatic changes in the uniformity and distribution of Ge nanostructures self-assembled on Si.