Water pollution is a challenging problem encountered in total environmental development. Near-infrared (NIR) spectroscopy is a well-refined technology for rapid water pollution detection. Calibration models are established and optimized to search for chemometric algorithms with considerably improved prediction effects. Machine learning improves the prediction capability of NIR spectroscopy for the accurate assessment of water pollution. Least squares support vector machine (LSSVM) algorithm fits parameters to target problems in a data-driven manner. The modeling capability of this algorithm mainly depends on its kernel functions. In this study, the LSSVM method was used to establish NIR calibration models for the quantitative determination of chemical oxygen demand, which is a critical indicator of water pollution level. The effects of different kernels embedded in LSSVM were investigated. A novel kernel was proposed by using a logistic-based neural network. In contrast to common kernels, this novel kernel can utilize a deep learning approach for parameter optimization. The proposed kernel also strengthens model resistance to over-fitting such that cross-validation can be reasonably utilized. The proposed novel kernel is applicable for the quantitative determination of water pollution and is a prospective solution to other problems in the field of water resource management.