Submergence, whether partial or complete, imparts some serious consequences on plants grown in flood prone ecosystems. Some plants can endure these conditions by embracing various survival strategies, including morphological adaptations and physiological adjustments. This review summarizes recent progress made in understanding of the stress and the acclimation responses of plants under waterlogged or submerged conditions. Waterlogging and submergence are often associated with hypoxia development, which may trigger various morphological traits and cellular acclimation responses. Ethylene, abscisic acid, gibberellic acid and other hormones play a crucial role in the survival process which is controlled genetically. Effects at the cellular level, including ATP management, starch metabolism, elemental toxicity, role of transporters and redox status have been explained. Transcriptional and hormonal interplay during this stress may provide some key aspects in understanding waterlogging and submergence tolerance. The level and degree of tolerance may vary depending on species or climatic variations which need to be studied for a proper understanding of waterlogging stress at the global level. The exploration of regulatory pathways and interplay in model organisms such as Arabidopsis and rice would provide valuable resources for improvement of economically and agriculturally important plants in waterlogging affected areas.