Soybean represents a valuable source of food for humans and animals and the quality of the seeds has great importance for the establishment and high productivity of this crop. Soybean seeds require continuous improvement, which is dependent on a better understanding of the regulatory mechanisms that coordinate seed germination. To investigate whether the method of water absorption into soybean seeds could lead to abnormal seedlings, and if this could be associated with cytogenetical consequences, we premoistened the seeds of three cultivars; M 6410 IPRO, M6210 IPRO, and BMX Potência RR by direct immersion (fast method), use of a wet substrate (intermediate method), and by moist atmosphere (slow method) with distilled water at 25ºC for 24 hours. We investigated the normal and abnormal seedlings, electrical conductivity, mitosis, cell death, and the chromosomal abnormalities index. The comet assay was applied to investigate DNA fragmentation. Direct immersion in water induced seedling growth inhibition and caused cytological alterations associated with genotoxicity effects in the studied soybean genotypes. Slow premoistening of the seeds increased seedling performance as a result of higher final germination percentage (above 85%), reduced abnormal seedlings (below 5%, on average), and reduced the electrical conductivity of seeds. All three genotypes of soybean seeds lost their ability to withstand the imbibitional damage induced by direct immersion as abnormal seedlings increased. We concluded that the fast water absorption by seeds poses a threat to genomic integrity owing to its potential for genotoxicity to DNA, manifesting as breaks or loss of whole chromosomes. Slow premoistening of the seeds resulted in a longer time period to deal with damage. Stabilized seedling growth was provided by altering cytogenetic responses during uptake of water by soybean seeds through the maintenance of cell viability.