A cruise was commissioned in the summer of 2009 to evaluate water quality in the Pearl River Estuary (PRE). Chemometrics such as Principal Component Analysis (PCA), Cluster analysis (CA) and Self-Organizing Map (SOM) were employed to identify anthropogenic and natural influences on estuary water quality. The scores of stations in the surface layer in the first principal component (PC1) were related to NH₄-N, PO₄-P, NO₂-N, NO₃-N, TP, and Chlorophyll a while salinity, turbidity, and SiO₃-Si in the second principal component (PC2). Similarly, the scores of stations in the bottom layers in PC1 were related to PO₄-P, NO₂-N, NO₃-N, and TP, while salinity, Chlorophyll a, NH₄-N, and SiO₃-Si in PC2. Results of the PCA identified the spatial distribution of the surface and bottom water quality, namely the Guangzhou urban reach, Middle reach, and Lower reach of the estuary. Both cluster analysis and PCA produced the similar results. Self-organizing map delineated the Guangzhou urban reach of the Pearl River that was mainly influenced by human activities. The middle and lower reaches of the PRE were mainly influenced by the waters in the South China Sea. The information extracted by PCA, CA, and SOM would be very useful to regional agencies in developing a strategy to carry out scientific plans for resource use based on marine system functions.