Water stress (drought and flood) is one of the major factors that limits sugarcane growth and yield. The two greenhouse experiments were conducted at Khon Kaen University, Thailand. The first experiment investigated the individual and combined effects of droughts and floods on two sugarcane cultivars. The results showed that photosynthetic potential, based on chlorophyll a fluorescence (PSII) and chlorophyll content, exhibited a response to the water regime treatments. However, stomatal conductance in the K93-219 cultivar was higher than the KK3 cultivar. Similarly, plant height, number of tillers, number of stems, fresh stem weight, and sugar quality were not affected by the varying water regime conditions imposed on both of the sugarcane cultivars. However, drought or flood conditions, whether alone or in combination, reduced the fresh stem weight, with regards to the water regimes and cultivars. In general, a combination of drought and flood reduced the fresh stem weight as opposed to drought or flood alone. The KK3 cultivar gave a higher fresh stem weight than the K93-219 cultivar under dual stress conditions. The second experiment investigated the auxin application rates at different growth stages on two sugarcane cultivars under flood conditions. The results revealed that the application of auxin at 10 mg L−1 increased the number, and fresh weight, of adventitious roots over the control (0 mg L−1). The cultivar K93-219 produced a higher number, and fresh weight, of adventitious roots. However, the amount of aerenchyma in the adventitious roots was not affected by auxin application rates, growth stages, or cultivars. Similarly, plant height, leaf width, number of stems, fresh stem weight, and sugar quality were not affected by auxin rates. Auxin application at five months of age increased leaf width and fresh stem weight over the control. The cultivar K93-219 tended to produce a higher fresh stem weight than the KK3 cultivar.