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Principal component analysis (PCA) were applied to assess surface water quality of the Songhuajiang River basin, China. Thirteen physical-chemical parameters in 25 stations were collected monthly during the period of 2008. Three factors were extracted by PCA, which explained 83.79% of the total variance. The first factor (PCA1) was positive correlated with permanganate index, BOD 5 , NH 3 -N, COD Cr , TN, and had negative loading on DO. The second factor (PCA2) captured variables of heavy metals, while pH, petroleum accounted for the greatest loading for factor 3(PCA3). Twenty five monitoring sites were clustered into three clusters based on 9 water quality parameters which were exceeded the water quality standards. The GIS maps of point source pollution yield and fertilizer pollution yield, together with water monitoring sites were applied to identify the main pollution sources. Industrial wastewater, agricultural activities and urban runoff influenced most of water quality variables. In high pollution area and moderate pollution area, multiple source pollution dominated. In low pollution area, the main pollution source was non-point source. These results provide information that can help local government to make better pollution control strategies for the Songhuajiang River basin.