Abstract Long–time prediction of water quality indicator such as chlorophyll–a (Chl–a) is crucial for water process engineering and environmental management. In order to capture the characteristics of long–time series and reduce the limitations of traditional long–time prediction strategies, this paper proposes a novel hybrid model by combining data decomposition, phase space reconstruction, feature fusion and improved WaveNet. Firstly, the original data is decomposed into several subsequences through time series decomposition. Then, the subsequences with chaotic characteristics are integrated with multiple features for phase space reconstruction. Next, the decomposed and reconstructed subsequences are fed back into the improved WaveNet model separately. Finally, the prediction results are obtained by summing the predicted values of the subsequences. In this paper, the reliability of the method is assessed using the dissolved oxygen, water temperature, pH and Chl–a data of a monitoring station in the Beihai coastal sea area, ablation experiments are conducted to demonstrate the effectiveness of each module in the proposed model, and comparisons with multiple benchmark and hybrid models show that the proposed model exhibits better performance in long–time prediction of coastal water quality in the next fourteen days.