A sequential injection analysis (SIA) system for the determination of NO3− ions using a microfluidic polymer chip with an embedded NO3− ion-selective electrode (NO3−-ISE) as a detector was developed. Under the optimal flow conditions of the SIA system, the NO3−-ISE showed a good linear relationship between peak heights and logarithmic concentrations of NO3− ions with a Nernstian slope of 57.1 mV per decade in a concentration range from 1.0 × 10−5 to 1.0 × 10−1 mol dm−3. Sample throughput of the present system for the determination of NO3− ions was ca. 12 samples per h. The proposed SIA system was applied to the determination of the level of NO3− ions in environmental water samples, such as tap water, well water and river water.