Excess soil moisture induces hypoxic conditions and causes waterlogging injury in soybean [Glycine max (L.) Merr.]. This study investigated the mechanism underlying the development of waterlogging injury. Nine Japanese soybean cultivars with varying degrees of waterlogging tolerance were grown in a hydroponic system for 14 days under hypoxic conditions. Shoot and root biomasses and root hydraulic conductivity were measured at an early vegetative stage for plants under control and hypoxic conditions. Root morphological traits and intramembrane aquaporin proteins were also analyzed. The tolerance of each cultivar to field waterlogging was based on biomass changes induced by the hypoxia treatment. Root hydraulic conductivity responses to hypoxia were associated with changes in total dry weight, leaf dry weight, and leaf area. The effects of hypoxic conditions on root hydraulic conductivity were also represented by the changes in root morphology, such as total root length, thick-root length, and number of root tips. Additionally, a 32.3 kDa aquaporin-like protein seemed to regulate root hydraulic conductivity. Our results from a hydroponic culture suggest that the soybean cultivar-specific responses to hypoxic conditions in the rhizosphere reflect fluctuations in hydraulic conductivity related to root morphological or qualitative changes.