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Elevation can greatly affect both intensity and duration of flooding in riparian areas, and may thus affect the performance of plants distributed therein. However, few studies have examined the performance of riparian plants over elevation difference. This study compared growth and reproductive traits of populations of the riparian species Polygonum hydropiper distributed at low and high elevations of 10 different riparian locations in the hydro-fluctuation belt of the Three Gorges Reservoir Region, China. Both the location and the interaction between location and elevation had significant effects on almost all growth and reproduction traits of P. hydropiper, suggesting that the effects of elevation varied greatly among different locations. Across all locations, high-elevation plants had significantly higher total biomass, stem biomass, root biomass, and plant height than low-elevation plants. Correspondingly, high-elevation plants also had significantly higher stem starch concentrations. In comparison, low-elevation plants had significantly lower biomass, shorter height, and thinner leaves; while they had significantly higher reproductive allocation, as well as faster germination and higher germination rate at a number of locations. Therefore, low energy consumption and high reproductive capacity could be a survival adaption of low-elevation plants to frequent and deep flooding. Local conditions and/or flooding might impose strong selection pressure on P. hydropiper, thus resulting in intra-specific differentiation. Across all locations, low- and high-elevation populations exhibit different growth and reproduction responses to different flooding regimes.