Soybean seeds are prone to flooding injury just after planting if they are exposed to excess moisture. We investigated the flooding tolerance of soybean seeds to clarify the relationship between flooding injury and imbibition, to identify factors that could provide fundamental information for the breeding of flooding-tolerant cultivars. Seven cultivars were used for this study. The seeds were geminated in a paper towel after a flooding treatment and then evaluated for survival. The imbibition of submerged seeds (passive imbibition) was evaluated as the seed fresh weight change during the flooding process. The imbibition of seeds with capillary effect (capillary imbibition) was measured by the bottom water supply method. Furthermore, the conductivity of the seed coat and seed osmolarity were measured. After 3 h of flooding, significant differences in survival were detected among cultivars. In addition, the passive imbibition during 10–30 min of flooding, and the capillary imbibition during 0–10 min of flooding were caused by significant differences in the imbibition rate among cultivars. Although neither imbibition showed a significant correlation with the survival directly, the ratio between the passive and the capillary imbibition rate was significantly correlated with survival. Factors affecting imbibition included the hydraulic conductivity of the seed coat and seed osmolarity, which were significantly correlated with the passive and the capillary imbibition rate, respectively. Thus, the balance between the capillary and passive imbibition behaviour of seeds, affected by the hydraulic conductivity of the seed coat and seed osmolarity, was closely correlated with the occurrence of flooding injury in soybean seeds.