Xanthium sibiricum, an annual weed, unexpectedly and dramatically occupied the exposed drawdown area after water had been impounded for the first time in the newly created Three Gorges Reservoir in China. In order to explain this phenomenon and establish an appropriate management strategy, the effects of constant submersion on seed viability and germination of X. sibiricum were investigated at two constant temperature regimes (25°C and 30°C) under artificial laboratory conditions. The results indicated that the seeds of X. sibiricum exhibited a high level of tolerance of submersion and up to 99% of seeds were viable in each treatment regime. The effect of submersion on germination was not obvious at 25°C until the submersion was prolonged for 180 days, while at 30°C the eventual germination rate of X. sibiricum, even after submergence for only one day, was significantly improved. The speed of germination was also consistently accelerated by prolonged periods of submersion. The proportion of seeds that germinated in all treatments combined was less that 56% due to seed dimorphism, thereby providing a seed bank. We conclude that the interaction between long-term winter flooding and high temperature in summer is the major reason that X. sibiricum was able to occupy the newly exposed drawdown area in the absence of competition. These findings provided further insight into how germination strategy and reservoir water-management regime contributed to this dramatic species outbreak.