Accurate water quality predictions are critical for water resource protection, and dissolved oxygen (DO) reflects overall river water quality and ecosystem health. This study proposes a hybrid model based on the fusion of signal decomposition and deep learning for predicting river water quality. Initially, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) is employed to split the internal series of DO into numerous internal mode functions (IMFs). Subsequently, we employed multi-scale fuzzy entropy (MFE) to compute the entropy values for each IMF component. Time-varying filtered empirical mode decomposition (TVFEMD) is used to further extract features in high-frequency subsequences after linearly aggregating the high-frequency sequences. Finally, support vector machine (SVM) and long short-term memory (LSTM) neural networks are used to predict low- and high-frequency subsequences. Moreover, by comparing it with single models, models based on 'single layer decomposition-prediction-ensemble' and combination models using different methods, the feasibility of the proposed model in predicting water quality data for the Xinlian section of Fuhe River and the Chucha section of Ganjiang River was verified. As a result, the combined prediction approach developed in this work has improved generalizability and prediction accuracy, and it may be used to forecast water quality in complicated waters.