Gravelly river channels are typical landscapes of the midstream, providing a unique habitat for pioneering species which are recently disappearing due to intensive vegetation colonization, eliminating the biodiversity and notably endangered species adapted to gravely habitat. Hence, disclose the reason and restoration strategies are highly demanded in many Japanese rivers. We hypothesized that the increment of vegetation cover is caused by the reduction of sediment as harvesting and trapping by dams. Areal photos of several rivers were analysed to obtain the period to re-colonize the vegetation after a flood, depending on the overlying sediment condition. Longer period was taken at the deposited sites, compared to non-deposited or eroded sites for re-colonization. Deposition of cleansed sediment which is low in moisture, nutrients and seeds, over the original substrate delayed the germination and the growth of vegetation. A dynamic model was developed to describe this processes (Asaeda et al., 2014) which consisted of four interacting modules; hydrological processes, trees, herbaceous plants and soil nutrient dynamic. It describes the recruitment and the growth of trees, herbaceous plant biomass, soil nitrogen concentration and vegetation flushing. The Simulation results well agreed with the observations of vegetation distribution and delay for re-colonization. Results with different sediment and hydrological conditions indicated the vegetation coverage is increased intensively by the decreasing fraction of deposited area, than the decreasing magnitude and frequency of floods. Therefore, it was concluded that the reduction of movable sediments in the river channel was the major cause for the recent intensive vegetation colonization.