In order to get a fully understanding of non-point pollution problem in rotation agricultural watershed at the central United States Illinois, USA, Principal component analysis (PCA) was used to do the water quality evaluation of the Little Vermilion River watershed. The PCA approach divided various factors that influence phosphorus transport into three principal components. The first component, botanical component, contained air temperature, cover phenotype, evapotranspiration, cover factor and dry mass factors. The second component contained precipitation and flow, which was defined as hydrologic component. The third component included tillage practices and nitrogen application, and was termed as anthropogenic component. The result showed that the hydrologic component impact phosphorus loss most than other components, especially for subsurface drainage water.