The landscape of a river sandbar is composed of several elements, including vegetation, bare areas, side-pools and so on. For sandy river management, it is necessary to determine the contributing factors for the ecosystem functions of alternate bar segments. In recent years, it has been reported that sandbars have a water purification function involving denitrification driven by sub-surface flow, but the details are still unknown. The objective of this study was to develop a model that could be used to examine how the nitrogen is trapped and retained by several elements of a sandbar in an alternate bar reach. We also developed a framework to analyze the temporal change in the denitrification by using a numerical simulation, aerial photos, and a water quality information system. The main results of this study are that the temporal change in the denitrification ecosystem function in a sandbar reach can be quantified using the proposed model and the denitrification activity has increased over the past 35 years. In addition, it was clearly shown that differences in the vegetation distribution and sandbar shape affect the nitrogen dynamics. Thus, the numerical simulation has made it possible to determine the most effective vegetation patterns to maximize the ecosystem function in a sandbar.