As a frontier of Sustainable Basin Research Initiative, we commenced a scenario-driven planning and evaluation research project which is to identify the strategic policy scenarios. As a part of the project, this study attempts to estimate the ecological impacts of land cover changes using landscape indices at the whole basin level. We analyzed spatio-temporal characteristics of natural area including forest, agricultural land, water area, barren which play an important role in nature-friendly sustainable watershed management. The results of analysis shelved that the size and diversity of natural area have been reduced, while patch number and isolation have been increased in proportion to urbanization in 1974, 1995 and four future scenarios in the Ara River Basin. Also, we estimated that the natural area could be conserved to some degree in the SD or DE scenarios with a concept of environment-friendly development and lifestyle. Various strategic environment policies may be evaluated and designed on the basis of the method, that is, scenario approach and landscape ecological analysis suggested in this study.