This paper proposes the quantitative evaluation method of the natural landuse based on small watersheds from the viewpoint of the water cycle, using GIS. Firstly, the existing landuse and the small watersheds from the common data (the spatial information that is digitally available) were prepared as basic data. The landuse data of 1955 were digitized from topographical map, and small watersheds were further classified into groups according to the two landuse dataset. Secondly, an indicator of the long-run average water flow of small watersheds and second level watersheds were calculated from the percolation. The transition of the landuse for every group of small watersheds was expressed numerically as the transition of the long-run average water flow. Therefore the quantitative evaluation of the watershed health of small watershed groups was made possible. Thirdly, the transitions of the environment of every second level watersheds were also evaluated with the indicator of the long-run average water flow and the six groups of small watersheds which were dispersed like mosaics in the watershed were analyzed. This made the examination of the conservation and restoration strategies for natural environments from the combination of the transitions of natural environment of different scales possible..