Main physiological changes experienced by plants during flooding stress. Oxygen (O2) depletion is the main direct effect produced by flooding. Poor soil aeration alters root energy metabolism due to the inhibition of the TCA cycle in the mitochondria and the stimulation of glycolysis and fermentation, which leads to the accumulation of toxic ethanol in roots. Hypoxia also leads to the inhibition of the aquaporin activity, which together with the altered root metabolism, contribute to stop the formation and elongation of lateral roots. Alterations in root functioning rapidly extend to the aerial parts, with hydraulic and chemical signals dominating the root to shoot communication. Low aquaporin activity and increased resistance to apoplastic water movement reduce xylem conductivity and, together with abscisic acid (ABA) accumulation in the leaves, enhance stomatal closure. Stomatal closure and impaired photosynthesis reduce CO2 uptake and the production of carbohydrates. Leaf chlorophyll concentration (chl) decreases due to photoinhibition and deficient root nitrogen uptake. The gaseous hormone ethylene is rapidly synthesised under hypoxic conditions in the roots, or in the leaves from its precursor ACC (1‐aminocyclopropane‐1‐carboxylate), causing leaf epinasty, reducing leaf growth, and inducing stomatal closure. Ethylene accumulation also leads to the formation of aerenchyma, which facilitates gas diffusion, suberin‐rich tissues, which prevent radial O2 loss (ROL), and hypertrophied lenticels, adventitious roots and pneumatophores, which favour O2 transport to submerged plant parts. Created with BioRender.com [Color figure can be viewed at wileyonlinelibrary.com]