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Changes in the timing of extreme precipitation have important ramifications for public safety and storm water management, but it has not received much attention in relation to flooding. This study analyzed the changes in the timing of extreme precipitation in the Poyang Lake basin and projected its future changes for the period 2020–2099. The study also quantified the influences of changes in the timing of peak flows on lake floods based on a hydrodynamic model. The results showed that peak rainfall in the Poyang Lake basin had occurred on later dates during the period 1960–2012, and it is this change that caused a delay in peak streamflows from five rivers in the lake basin. Moreover, the effects of these changes are expected to be more prominent during 2020–2099; for example, the rate of delay will be about 2.0 days per 10 years both for peak rainfall and for streamflow in the Poyang Lake basin. The hydrodynamic simulation further showed that a delay of peak streamflows from five rivers would significantly increase the flood level and outflow of the lake and also prolong the duration of floods. These results indicate that the risk of floods in Poyang Lake is likely to increase in the future, therefore making flood control in this region more challenging.