Land use change is a key factor affecting water resources and the environment; with the development of urbanization, hydrological processes in river basins have also changed. Although the research on land use change has been widely discussed, it focuses principally on changes to total area. In this study, we considered land-use density changes to be as important as area changes, including changes in the urban structure reflected by variations in building density and forest growth and replacement reflected by changes in canopy density and root depth. In this research, we demonstrate the importance of land use density changes in cities and forests and their impact on hydrological processes. It could mostly realistic studies of land use impacts on hydrology reflect aspects of both area and density. This research used the Soil and Water Assessment Tool (SWAT) to describe density changes with selected parameters and quantify the characteristics of these changes by combining remote sensing technology and mathematical methods. In results, SWAT produced good simulation results for a mixed basin with large cities and forest cover in western Japan and clearly reflects changes in the hydrological processes influenced by both area and density changes in land use. We show that (1) Urbanized areas increased by 13%, the surface runoff ratio increased by 7%, and the baseflow ratio was reduced by 13%; (2) The surface runoff ratio between the different cities in the basin has a discrepancy of 0.18 because of differences in the urbanization processes; and (3) Forest growth increases canopy water storage capacity, which in turn increases evapotranspiration. Additionally, root growth will have a negative impact on groundwater recharge. Consequently, the changing density of land use is an important factor that cannot be ignored when studying hydrological processes.