Accurate prediction of monthly runoff is critical for effective water resource management and flood forecasting in river basins. In this study, we developed a hybrid deep learning (DL) model, Fourier transform long short-term memory (FT-LSTM), to improve the prediction accuracy of monthly discharge time series in the Brahmani river basin at Jenapur station. We compare the performance of FT-LSTM with three popular DL models: LSTM, recurrent neutral network, and gated recurrent unit, considering different lag periods (1, 3, 6, and 12). The lag period, representing the interval between the observed data points and the predicted data points, is crucial for capturing the temporal relationships and identifying patterns within the hydrological data. The results of this study show that the FT-LSTM model consistently outperforms other models across all lag periods in terms of error metrics. Furthermore, the FT-LSTM model demonstrates higher Nash–Sutcliffe efficiency and R2 values, indicating a better fit between predicted and actual runoff values. This work contributes to the growing field of hybrid DL models for hydrological forecasting. The FT-LSTM model proves effective in improving the accuracy of monthly runoff forecasts and offers a promising solution for water resource management and river basin decision-making processes.