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The protection of water resources is of paramount importance to human beings' practical lives. Monitoring and improving water quality nowadays has become an important topic. In this study, a novel Bayesian probabilistic neural network (BPNN) improved from ordinary Bayesian probability methods has been developed to quantitatively predict water quality parameters including phosphorus, nitrogen, chemical oxygen demand (COD), biochemical oxygen demand (BOD), and chlorophyll a. The proposed method, based on conventional Bayesian probability methods, involves feature engineering and deep neural networks. Additionally, it extracts significant information for each endmember from combinations of spectra by feature extraction, with spectral unmixing based on mathematical and statistical analysis, and calculates each of the water quality parameters. The experimental results show the great performance of the proposed model with all coefficient of determination R 2 over 0.9 greater than the values (0.6–0.8) from conventional methods, which are greater than ordinary Bayesian probability analysis. The mean percent of absolute error (MPAE) is taken into account as an important statistical criterion to evaluate model performance, and our results show that MPAE ranges from 4% (nitrogen) to 10% (COD). The root mean squared errors (RMSEs) of phosphorus, nitrogen, COD, BOD, and chlorophyll-a (Chla) are 0.03 mg/L, 0.28 mg/L, 3.28 mg/L, 0.49 mg/L, and 0.75 μg/L, respectively. In comparison with other deep learning methods, this study takes a relatively small amount of data as training data to train the proposed model and the proposed model is then tested on the same amount of testing data, achieving a greater performance. Thus, the proposed method is time-saving and more effective. This study proposes a more compatible and effective method to assist with decomposing combinations of hyperspectral signatures in order to calculate the content level of each water quality parameter. Moreover, the proposed method is practically applied to hyperspectral image data on board an unmanned aerial vehicle in order to monitor the water quality on a large scale and trace the location of pollution sources in the Maozhou River, Guangdong Province of China, obtaining well-explained and significant results. [ABSTRACT FROM AUTHOR]