Nitrogen overload is one of the main reasons for the deterioration of surface water quality. Hence, monitoring nitrogen loadings is vital in maintaining good surface water quality. Increasingly, the use of spectral reflectance to monitor nitrogen concentration in water has shown potentials, but it poses some problems. Therefore, it is necessary to explore new methods of quantitative monitoring of nitrogen concentration in surface water. In this paper, hyperspectral data from surface water in the Ebinur Lake watershed are used to select sensitive bands using spectral transformation, the spectral index, and a coupling of these two methods. The particle swarm optimization support vector machine (PSO-SVM) model, constructed on the basis of sensitive bands, is used quantitatively to estimate the total nitrogen concentration in surface water and subsequently to verify its accuracy. The results show that the bands near 680, 850, and 940 nm can be used as sensitive bands for estimation of the total nitrogen concentration of surface water in arid regions. Compared with the best estimation models constructed by sensitive bands selected using the spectral transformation or the spectral index alone, the best model based on the coupling of these two measures is more accurate (R2 = 0.604, Root Mean Square Error (RMSE) = 1.61 mg/L, Residual Prediction Deviation (RPD) = 2.002). This coupling method leads to a robust, accurate, and strong predictability model, and can contribute to improved quantitative estimation of water quality indexes of rivers in arid regions.