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Nonpoint source (NPS) pollution has become one of the biggest challenges in maintaining water quality and aquatic ecosystems. However, the impacts of topography, land use change, human activities, precipitation etc., make the modeling and control of NPS pollution in temporal and spatial scales difficult. In recent years, the rapid development of Remote Sensing (RS) and Geographic Information System (GIS) technologies provide a new research method to investigate into NPS pollution. Since the construction of the Three Gorges Reservoir, the water flow of the reservoir slows down and the capability of water body self-purification is decreasing, consequently water quality of this area is getting worse due to the NPS pollution. In this paper, a methodology which based on RS and GIS for evaluating the NPS pollution was described and tested on the Ruxi River basin, which is a branch of Yangtze River basin in Three Gorges Project area, Southwestern China. Multi-temporal remote sensing images were used to analyze the variety of long-term land use change. GIS was used to characterize the sub-basins throughout the watershed for changes in land use and analyze multi-factor spatial relationship in NPS pollution. The Soil and Water Assessment Tool (SWAT) and a series of water quality data in the field were used to simulate the temporal-spatial features of total nitrogen (TN) and total phosphorus (TP). Research results indicate that the impacts of anthropic activities on landscape are intensive to NPS pollution. There is a strong relationship between slope, land cover, distance to the stream channel and NPS pollution.