The conservation of aquatic plants in river ecosystems should consider the wash-out (away) problem resulting from severe rainfall. The aquatic plant Schoenoplectus gemmifer is an endangered species endemic to Japan. Our previous study reported that the population size of S. gemmifer in Hamamatsu city, Japan, had decreased by one-tenth because many individuals had been washed out by a series of heavy rains in 2004. However, there is insufficient information on the ecological nature of this endangered aquatic plant for adequate conservation. In this paper, we report the population dynamics of one population in Hamamatsu city from 2004 to 2012 in relation to rainfall. We surveyed the number and growing location of all living individuals in the population 300 times during the study period. To examine the temporal changes of individual plants, we also counted the number of culms for 38 individuals in four observations among 300 records. Decreases and increases in the population size of this plant were associated with washing out and the settlement of gemmae (vegetative propagation), respectively. The major cause of the reduction in the population size was an increase in the number of washed-out individuals and not the decreased settlement of gemmae. The wash-out rates for small and large individuals were not significantly different. Small individuals having a stream form with linear leaves resisted flooding, and large individuals were often partially torn off by flooding events. Modification of river basins to reduce the flow velocity may be effective for the conservation of S. gemmifer.