It has been known that shallow-water regions, such as tidal flats, sea grass and sea weed beds have water purification capability, and they also serve as nursery grounds for many fishes. On the other hand, tidal flat areas are economically attractive sites for reclamation, to be used for developing industries. When developing shallow-water areas, we have to propose a plan to mitigate the environmental impact associated with such a development plan. However, it is difficult to estimate the affects on the ecosystem and water purification, and the literature related to this matter is insufficient. In order to evaluate the ability of coastal tidal flat and to predict the future changes, it is necessary to develop a reliable prediction technique and construction of data by using a field investigation. In this study, we carried out a numerical model test for the tidal flat ecosystem, using the pelagic system and the benthic system, simultaneously, in order to show a change in the tidal flat ecosystem. The flow of nitrogen, phosphorus and carbon has been identified as a primary consideration of marine ecosystem components, and the capability of water purification and the change of the tidal flat were predicted using this flow. In order to make a more reliable prediction, a field investigation to determine tide, current and creatures of the object coastal area has been done. The purification capability of this shallow-water region is estimated from the model results. According to the results of experiments, the tidal flat has a capability of water purification (Sink) of 11mgN/m2/day, but the other area has a load (Source) of 20mgN/m2/day. As a result, we could confirm that the tidal flat of an object coastal area plays an important role in water purification.