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Geographic informational system (GIS) and the Soil and Water Assessment Tool (SWAT) was used to simulate the transport of runoff, sediment, total nitrogen and total phosphorus into the Zhangjiafen stations. The main objective was to discuss climate change affecting on sediment and water quality. The results showed: The SWAT generally performs well and could accurately simulate monthly runoff, sediment, total nitrogen and total phosphorus yield with a Nash-Sutcliffe coefficient and a coefficient of determination of greater than 0.7 during calibration and validation. Climate change had large effect on runoff, followed by sediment, total nitrogen and total phosphorus.