The changes in water status of germinating and non-viable soybean (Glycine max L. Merr.) seeds were characterized by nuclear magnetic resonance (NMR) spectroscopy. There were distinct changes in water status between viable and non-viable soybean seeds. In dry seeds, there were only two components, bound and bulk water, as revealed by component analysis of NMR (T2) data. On the contrary, a three-component water proton system (bound, bulk and free water) was observed in both germinating and non-viable soybeans during Phase I of hydration. The bulk water component of non-viable seeds disappeared completely during the lag phase (Phase II) of hydration, resulting in a two-component water proton system. In contrast, the three-component water proton system in Phase II was observed in the germinating seeds. Rapid hydration (Phase III), following Phase II, was observed in germinating soybean seeds only. Due to reorganization of water protons, there was a concomitant increase in bulk and free water, but a decrease in bound water. The physical state of water in these seeds (analysed by NMR spectroscopy) and the measurements of tissue leachate conductivity suggest that non-viable soybean seeds were more affected by the disorganized cell structure in the seed membrane system. The present study also provides evidence that physical reorganization of water is essential in germinating soybean seeds during hydration.