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A SAG12:ipt gene construct, which increases cytokinin biosynthesis in response to senescence, was introduced into Arabidopsis plants to delay senescence induced by flooding stress. Two forms of flooding stress, including total submergence and root waterlogging, were applied to SAG12:ipt (IPT) and wild-type (WT) plants for 1, 3, and 5 d. A separate experiment compared the recovery of WT and IPT plants subjected to flooding stress. Biomass accumulation, carbohydrate and chlorophyll contents, and cytokinin and abscisic acid were quantified to compare genotypic responses to flooding stress and post-flooding recovery. Real-time RT-PCR studies were performed to quantify ipt and SAG12 gene expression. IPT plants exposed to waterlogging accumulated greater quantities of cytokinins more rapidly than WT plants or those exposed to total submergence. Cytokinin accumulation was accompanied by phenotypic adaptations, including chlorophyll retention and increased biomass and carbohydrate content relative to WT plants. Abscisic acid accumulated rapidly in WT and IPT plants under waterlogging stress but remained low in all genotypes exposed to total submergence. IPT plants showed improved recovery after waterlogging stress was removed. Expression of ipt in submerged plants did not result in cytokinin accumulation until submergence stress was removed. At that point, IPT plants accumulated greater quantities of cytokinin and recovered to a greater extent than WT plants. This study established the relationship between flooding tolerance and cytokinin accumulation in IPT plants and suggested that translation of ipt transcripts and subsequent cytokinin accumulation were delayed under submergence stress.