The seeds of the soybean Glycine max (L.) Merr. show high sensitivity to excessive water in the germination stage, and this susceptibility reduces germination rate, plant growth and yield. Therefore, it is important to determine the relationship between germination and water conditions. In this study, we investigated whether nuclear magnetic resonance (NMR) relaxation time (T_2) could be used to characterize germination in two soybean cultivars, 'Fukuyutaka' (yellow seed coat) and 'Wase-kurodaizu' (black seed coat), and one kidney bean cultivar, 'America-saito'. The germination index (GI) of 'Fukuyutaka' was the highest, followed by that of 'Wase-kurodaizu', and 'America-saito.' The water contents and T_2 values of long fraction in the two soybean cultivars increased faster than those in the kidney bean, and T_2 values more clearly explained the difference than water content. We also observed the digestion of seed storage substances. Starch granules were digested 72 hours after imbibition in the cotyledons of 'Fukuyutaka,' while still observed in those of 'Wase-kurodaizu' and 'America-saito.' Additionally, most oil bodies were digested in the cotyledons of 'Fukuyutaka,' while abundant oil bodies were still observed in those of 'Wase-kurodaizu' 72 hours after imbibition. This suggests that the difference in GI can be explained by water states indicated by NMR T_2 and the degradation of the storage substances of seeds after imbibition.