Incidents of flooding in tropical and subtropical fruit trees have increased as a result of climate change. Because of flooding, the anaerobic conditions of the rhizosphere increase the conditions for phytotoxicity and infection by pathogenic fungi and bacteria. Due to oxygen depletion in waterlogged soils, growth, functions of the roots and of the entire plant are impaired. The decrease in the photosynthetic rate is considerable because of the reduced functional leaf area because of chlorosis, necrosis, leaf drop and stomatal closure, as well as chlorophyll degradation. Plants have developed different morphological, physiological, and biochemical adaptations to survive hypoxic stress. Some fruit trees form an aerenchyma in roots for the diffusion of oxygen from the aerial parts. Induced aerenchyma-containing adventitious roots, rapidly elongate stems into deeply flooded soils; or they form hypertrophied lenticels, like some mango varieties. Measures for better adaptations and tolerance of tropical fruit trees to climatic impact include the following: adaptations of the cultivated terrain, selection of varieties, rootstocks more tolerant to hypoxic stress, pruning to reestablish the balance of the aerial part/roots, and foliar applications (e.g., of glycine betaine or hydrogen peroxide (H2O2)). Mycorrhizal colonization of roots can increase tolerance to waterlogging, while the application of fertilizers, such as CaO or MgO, can improve the redox potential of flooded soils. We present results of studies on this problem for the following fruits: yellow passion fruit (Passiflora edulis f. flavicarpa) and purple passion fruit (P. edulis f. edulis), cape gooseberry (Physalis peruviana), lulo or naranjilla (Solanum quitoense), tree tomato (Solanum betaceum), citrus (Citrus spp.), guava (Psidium guajava), papaya (Carica papaya), and mango (Mangifera indica).