Under transient waterlogging, a number of transformations in the soil are generated associated with lack of aeration, seriously affecting the root system. Significant progress has been reported on understanding the effects of lack of oxygen on the metabolism of the roots, although few studies have examined changes in the soil. Diverging conclusions about the degree of tolerance exhibited by plants exclude the effects of hypoxia and anoxia on physical-chemical soil properties under plant experiments. This review examines the main changes occurring in soil and roots due to transient soil waterlogging conditions. Parameters such as antioxidant capacity, nutrient uptake dynamics and regeneration and distribution of the root system are relevant for selecting rootstocks tolerant to soil waterlogging.