Partial or complete submergence of shoots of rice (Oryza sativa L.) poses a dual challenge: the roots have to function in anoxic soil and gas exchange between shoots and air becomes restricted to a small aerial portion or is abolished during complete submergence. Adaptation of roots to anoxic and chemically reduced waterlogged soils was reviewed by Kirk et al. (Prog Bot, 2014). With deeper floods the O-2 provision to the roots may decline, because there is a high resistance for gas exchange between floodwater and the submerged part of the foliage. Floodwaters differ greatly in light levels and CO2 concentrations, thus restricting underwater photosynthesis by varying degrees. During the day, underwater photosynthesis largely determines the O-2 concentrations within submerged rice, whereas, at night, tissue O-2 declines, particularly so in roots. Deepwater rice establishes a 'snorkel' via elongation of aerenchymatous internodes and leaf sheaths; these responses are triggered by ethylene, which acts on two Snorkel genes encoding ethylene-responsive factor (ERF) transcriptional regulators to elicit the action of gibberellin. In addition, aquatic roots emerge from stem nodes. Perversely, pronounced shoot elongation can be catastrophic for lowland rice completely submerged during transient floods. In these circumstances tolerance is underpinned by suppression of elongation by SUB1A-1, an ERF transcriptional regulator that blocks ethylene responsiveness. However, many aspects of survival during transient complete submergence remain unclear, such as the role of carbohydrate depletion, photosynthesis under water, and anoxia tolerance in roots. After desubmergence, possible injury to shoots from water deficits and free radicals also requires further elucidation. This review is focused on the evaluation of the physiological mechanisms involved in the acclimation-adaptation of rice to these floods.