The effects of the Yangtze River source of drinking water on metabolites of mouse (Mus musculus) were implemented to observe the environmental health issue of the water by use of the 1H nuclear magnetic resonance (NMR) spectroscopy-based metabonomics. All the sampled mice were treated for 90 days. There were 20 organic pollutants discovered in the water with total concentration of 9.41 microg/l. The NMR spectra for the sampled mice were different at delta2.06, delta2.24 and delta5.22. The concentrations of alanine, glycoprotein, acetone and trimethylamine-N-oxide in the source water group mice were decreased but that of creatinine and glucose were increased, which indicated that hepatotoxicity and kidney dysfunction occurred. There were six parameters for the source water group mice were different or extremely different from that of the control group. And these metabolites are responsible for separation of the data along PC1 and PC2 which may be used as biomarkers to indicate the source water pollution. The results indicate that 1H NMR-based metabonomic approach is a useful technique to test toxicity of xenobiotics on metabolites for observation of the environmental health issue of source water.