In order to anticipate residual errors and improve accuracy while reducing uncertainties, this work integrates the long short-term memory (LSTM) with the Soil and Water Assessment Tool (SWAT) to create a deep learning (DL) model that is guided by physics. By forecasting the residual errors of the SWAT model, the SWAT-informed LSTM model (LSTM-SWAT) differs from typical LSTM approaches that predict the streamflow directly. Through numerical tests, the performance of the LSTM-SWAT was evaluated with both LSTM-only and SWAT-only models in the Upper Heihe River Basin. The outcomes showed that the LSTM-SWAT performed better than the other models, showing higher accuracy and a lower mean absolute error (MAE = 3.13 m3/s). Sensitivity experiments further showed how the quality of the training dataset affects the performance of the LSTM-SWAT. The results of this study demonstrate how the LSTM-SWAT may improve streamflow prediction greatly by remote sensing and in situ observations. Additionally, this study emphasizes the need for detailed consideration of specific sources of uncertainty to further improve the predictive capabilities of the hybrid model.