In plants, dormancy is induced by numerous environmental stressors. In Hainan's tropical climate, dormancy is crucial for the repropagation of water lily plants, and the tubers emerging from dormancy can produce 3–5 plantlets; however, tropical water lilies often resist entering this stage even in cold and short-day conditions, leading to frost injuries and death. In this study, we employed the floating starvation method (FSM) to induce nutritional deficiency, driving tropical water lily plants into dormancy. We examined the effects of various durations of FSM (0, 13, 26, and 40 days) on Nymphaea atrans plants. Our results indicated that nutritional stress was essential for inducing dormancy in N. atrans, with plants beginning to enter dormancy after approximately 40 days of treatment. During this period, the dry matter content of the tubers significantly increased, unlike in the leaves, suggesting an enhanced allocation of underground resources in response to nutrient stress. The tubers accumulated substantial amounts of carbohydrates, soluble sugars, and starch, providing the energy needed to break dormancy during subsequent growth. Increases in free proline, as well as and the activities of antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and malondialdehyde (MDA), indicated that N. atrans initiated an active oxygen-scavenging system to mitigate oxidative stress. A notable increase in abscisic acid (ABA) content was observed, accompanied by a decrease in gibberellic acid (GA3) and indole-3-acetic acid (IAA) levels. This prolonged nutritional stress significantly increased ABA levels, leading to leaf and stem abscission and a reduction in GA3 and IAA through decomposition, finally resulting in dormancy. These findings provide new insights into the potential regulatory mechanisms of tuber dormancy induction through FSM in N. atrans.