Climate change is thoroughly linked to shifts in precipitation patterns and an increased frequency of flooding events. Flooding stress has emerged as a significant hazard to important oilseed crops, adversely impacting plant growth and development. Oxygen availability to plant roots is severely limited during waterlogged stress, resulting in hypoxic or anoxic environments. To manage such stresses, plants initiate a range of physiological, morphological, and biochemical adaptations, including the development of adventitious roots (ARs) and aerenchyma tissues, as well as the regulation of endogenous hormones and metabolites. Phytohormones are key modulators of plant adaptation to waterlogging stress, where their interactions strongly influence plant resilience. Critical genes and signaling pathways orchestrate these adaptive responses. Recent research has highlighted the intricacy of these phytohormone responses and the potential to exploit this knowledge to enhance crop tolerance. By understanding the precise roles of hormones such as ethylene, abscisic acid, and gibberellins, scientists are uncovering new strategies for mitigating the damaging impacts of waterlogging. Additionally, there is increasing interest in using phytohormones as exogenous treatments to strengthen plant defenses against flooding. Molecular studies have advanced our knowledge of the underlying metabolic pathways and target genes that enhance plant flooding tolerance. However, more research is required to fully elucidate the genetic regulation and functionally characterize all of the genes related to flooding tolerance. Additionally, innovative methods such as gene and genome editing and advanced breeding approaches hold promise for developing varieties with enhanced tolerance to waterlogging. This chapter provides a comprehensive review of the molecular mechanisms governing plant responses to waterlogging, focusing on the role of phytohormones on plant growth, development, and productivity of oilseed crops. Future research challenges and opportunities are also discussed, particularly in developing climate-resilient agricultural systems.