Watershed ecosystems are watershed-scale ecosystems that can be divided into two subsystems:land ecosystems and aquatic ecosystems.These two systems interact tightly through hydrology cycle.Aquatic ecosystems obtain water with nutrients from land ecosystems through hydrology cycle in watersheds.Aquatic ecosystems are often damaged by nonpoint source and point source pollution from land ecosystems.Nonpoint source pollution occurs coupling with watershed runoff,and it contributes a significant portion of all pollutants entering surface waters.Watershed-based water quality management must be taken into consideration and a tool is demanded to assess the impact of management on water supplies and nonpoint source pollution in watersheds and river basins.This paper introduces the methodology and practice in building watershed-based systems for integrated management of surface water quality.The general components of the systems comprise mathematics simulation models,GIS and aquatic ecosystem assessment system.All components are imbedded in an integrated structure that takes advantage of the GIS’s open architecture.Four major processes are modeled in management systems:hydrology cycle,soil erosion process and transport of nutrients and dynamics of water quality in water bodies.Aquatic ecosystem assessment is suggested to be taken into consideration in all of the further development of management systems,for natural and anthropogenic disturbances that occur in watersheds not only impact surface water quality,but whole aquatic ecosystems as well.