When crop plants are subjected to soil waterlogging, or an anaerobic condition, their root and shoot systems respond differently. A variety of morphological and anatomical alterations develop in the root system. Reduction of the root respiration rate has been reported in both flooding-tolerant and intolerant species. Besides alcoholic fermentation, several diverse fermentative bypasses take place, which ameliorate the poisoning through excessive accumulation of specific metabolic intermediates. Root systems starved of oxygen are also poor providers of mineral nutrients for both themselves and the shoot systems. Stomatal closure and non-stomatal metabolic alterations are responsible for the reduction of leaf CO2 incorporation. Plant hormones are much involved in regulation of these physiological adaptations.