Accurately predicting the concentration of organochlorine pesticides (OCPs) presents a challenge due to their complex sources and environmental behaviors. In this study, we introduced a novel and advanced model that combined the power of three distinct techniques: Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN), Variational Mode Decomposition (VMD), and a deep learning network of Long Short-Term Memory (LSTM). The objective is to characterize the variation in OCPs concentrations with high precision. Results show that the hybrid two-stage decomposition coupled models achieved an average symmetric mean absolute percentage error (SMAPE) of 23.24 % in the empirical analysis of typical surface water. It exhibited higher predictive power than the given individual benchmark models, which yielded an average SMAPE of 40.88 %, and single decomposition coupled models with an average SMAPE of 29.80 %. The proposed CEEMDAN-VMD-LSTM model, with an average SMAPE of 13.55 %, consistently outperformed the other models, yielding an average SMAPE of 33.53 %. A comparative analysis with shallow neural network methods demonstrated the advantages of the LSTM algorithm when coupled with secondary decomposition techniques for processing time series datasets. Furthermore, the interpretable analysis derived by the SHAP approach revealed that precipitation followed by the total phosphorus had strong effects on the predicted concentration of OCPs in the given water. The data presented herein shows the effectiveness of decomposition technique-based deep learning algorithms in capturing the dynamic characteristics of pollutants in surface water.