A flow injection-capillary electrophoresis (FI-CE) method was developed by sample automatic introduction with FI-CE interface. The experimental parameters such as detection wavelength, concentration of electroosmotic flow modifier and tetraborate sodium in carrier, pH of the carrier, carrier flow-rate and sample loop volume were optimized. The effects of common anions in environmental water were studied and no interference was observed. The detection limits of nitrate of 0.2 mg/L and nitrite of 0.4 mg/L (3sigma) were obtained with 50 muL sample volume. The relative standard deviations (RSD) of peak height are 1.6% and 2.0% (20mg/L, n=25), and the peak area RSD are 1.7% and 1.6% (20 mg/L, n=25), respectively at a sampling frequency of 60/h. This method was applied to analyze well water samples, the results were in good agreements with those obtained by ion chromatography (IC). The recoveries in well water samples by spiked with 10 mg/L nitrate and nitrite were between 98% and 108%.