Based on isotope labelling, we found that liquid water can afford an ultrafast permeation through graphene-based nanochannels with a diffusion coefficient 4–5 orders of magnitude greater than in the bulk case. When dissolving ions in sources, the diffusion coefficient of ions through graphene channels lies in the same order of magnitude as water, while the ion diffusion is slightly faster than water, indicating that the ions are mainly transported by water flows and the delicate interactions between ions and nanocapillary walls also take effect in the accelerated ion transportation.