This paper described the overall operations and applications of the water environment management and evaluation systems (WEMES) for environmental management, conservation, and evaluation for a small watershed. WEMES was to be applied with field data from small watersheds ranging from 0.4 to 29.79km2 in size which have steep topography and complex landuses. WEMES was a computer aided decision support system, that was comprised of the database subsystem, the simulation model subsystem, the environmental evaluation model subsystem, and the graphic user interface subsystem that visualizes the simulated results. The water environment management and evaluation with WEMES was successfully performed.