Clean water is an indispensable essential resource on which humans and other living beings depend. Therefore, the establishment of a water quality prediction model to predict future water quality conditions has a significant social and economic value. In this study, a model based on an artificial neural network (ANN), discrete wavelet transform (DWT), and long short-term memory (LSTM) was constructed to predict the water quality of the Jinjiang River. Firstly, a multi-layer perceptron neural network was used to process the missing values based on the time series in the water quality dataset used in this research. Secondly, the Daubechies 5 (Db5) wavelet was used to divide the water quality data into low-frequency signals and high-frequency signals. Then, the signals were used as the input of LSTM, and LSTM was used for training, testing, and prediction. Finally, the prediction results were compared with the nonlinear auto regression (NAR) neural network model, the ANN-LSTM model, the ARIMA model, multi-layer perceptron neural networks, the LSTM model, and the CNN-LSTM model. The outcome indicated that the ANN-WT-LSTM model proposed in this study performed better than previous models in many evaluation indices. Therefore, the research methods of this study can provide technical support and practical reference for water quality monitoring and the management of the Jinjiang River and other basins.