In flow-regulated rivers, natural flow patterns and related sedimentation processes are disturbed, thus interrupting the magnitude and duration of spates. We hypothesized that this in turn might alter the impact of spates on plant communities inhabiting sandbars along the river channel. In order to test this hypothesis, the effects of spates of different magnitudes and durations on spatial variation and composition of a Phragmites japonica Steud. community on a sandbar during a 2-year period were investigated. The flow variation of the river was continuously monitored, and the spates were categorized as small, medium or large, based on the magnitude (depth). Growth parameters (shoot length and shoot density), above-and belowground biomass of the plant community and the quantity of litter retained within selected quadrats, and ash-free dry weight (AFDW) of the soil were observed at seven different locations: two each at the extreme upstream, middle and extreme downstream and one location in the downstream reaches of the sandbar. Our results showed that the aboveground biomass declined due to large-scale spates; however, these spates triggered the formation of secondary shoots if sediments were accumulated as a result of the spates. Conversely, the aboveground biomass did not recover if the substrate was eroded. Accumulated litter beneath shoots was easily washed away due to spates, positively affecting shoot re-growth. The effects of spates on the P. japonica plant community depended highly on the location of the plants on the sandbar and the magnitude and duration of the spates. The different erosion-sedimentation processes, depending on the local river channel morphology and spate types, significantly affected the growth and morphological characteristics of P. japonica population.