During shortcut biological nitrogen removal in a polluted river, total nitrogen, ammonia nitrogen and nitrite nitrogen were quantified by near infrared spectroscopy and the synergy interval partial least squares (siPLS) algorithm. Spectral data of 138 water samples were obtained with a near infrared spectrometer. In addition, the real values of total nitrogen, ammonia nitrogen and nitrite nitrogen were measured with traditional chemical methods. SiPLS analysis models of total nitrogen, ammonia nitrogen and nitrite nitrogen were built through the siPLS algorithm based on spectral data and real values. The results obtained from the siPLS analysis model of total nitrogen revealed that, when the full spectra were divided into 19 intervals, the combination of the 7^th, 12^th and 19^th subintervals yielded the best model. The correction coefficient (R_p) is 0.9931, with the root mean squared error of calibration (RMSECV) being 1.7869. The results obtained from the siPLS analysis model of ammonia nitrogen indicated that, when the full spectra were divided into 16 intervals, the combination of the 1^st, 7^th, 15^th and 16^th subintervals yielded the best model. The R_p is 0.9947 and the RMSECV is 1.3419. For nitrite nitrogen, the siPLS analysis model indicated that, when the full spectra were divided into 16 intervals, the combination of the 7th and the 11th subintervals yielded the best model. The R_p and RMSECV was 0.9951 and 1.0518. These findings demonstrated that the proposed approach may effectively analyze the concentrations of total nitrogen, ammonia nitrogen and nitrite nitrogen during the treatment of a polluted river based on shortcut biological nitrogen removal. This approach, which is based on near infrared spectroscopy, is fast and accurate for the detection of different types of nitrogen in water.