Slow seed germination and delayed seedling establishment will become a major problem for rice production in flood-prone lowland areas as sowing method shifts from transplanting to direct seeding. To address this problem, the relationships between genotypic differences in the pattern of water uptake over different times of seed imbibition and adaption to anaerobic conditions were studied. The pattern of water uptake and germination time under aerobic and anaerobic conditions was evaluated for fifty-eight contrasting rice genotypes. Among them, nine lines had been developed for anaerobic germination (AG) and submergence tolerance (Sub1) by the International Rice Research Institute. In addition FR13A, with a designated Sub1 gene and IR42 without the Sub1 gene were used as model genotypes. Results showed that cluster analysis separated the genotypes into three groups based on the water content in seeds at different times of seed imbibition. Most AG+Sub1 lines were placed in cluster 3 which was characterized by rapid water uptake during the first 48 h of seed imbibition and rapid germination under aerobic and anaerobic conditions. Cluster 1 and 2 included genotypes with slower water uptake during the first 48 h and between 96 and 120 h of seed imbibition compared with cluster 3 under anaerobic condition. Therefore, these genotypes germinated more slowly than AG+Sub1 lines. The significant variation between two model genotypes in germination time was not significant under anaerobic condition. The present results verified that the regulation of water uptake during rice seed imbibition play an important rule in germination ability of rice seeds under anaerobic conditions.