Neural networks have become widely employed in streamflow forecasting due to their ability to capture complex hydrological processes and provide accurate predictions. In this study, we propose a framework for monthly runoff prediction using antecedent monthly runoff, water level, and precipitation. This framework integrates the discrete wavelet transform (DWT) for denoising, variational modal decomposition (VMD) for sub-sequence extraction, and gated recurrent unit (GRU) networks for modeling individual sub-sequences. Our findings demonstrate that the DWT-VMD-GRU model, utilizing runoff and rainfall time series as inputs, outperforms other models such as GRU, long short-term memory (LSTM), DWT-GRU, and DWT-LSTM, consistently exhibiting superior performance across various evaluation metrics. During the testing phase, the DWT-VMD-GRU model yielded RMSE, MAE, MAPE, NSE, and KGE values of 245.5 m3/s, 200.5 m3/s, 0.033, 0.997, and 0.978, respectively. Additionally, optimal sliding window durations for different input combinations typically range from 1 to 3 months, with the DWT-VMD-GRU model (using runoff and rainfall) achieving optimal performance with a one-month sliding window. The model's superior accuracy enhances water resource management, flood control, and reservoir operation, supporting better-informed decisions and efficient resource allocation.