Predicting streamflow is essential for managing water resources, especially in basins and watersheds where snowmelt plays a major role in river discharge. This study evaluates the advanced deep learning models for accurate monthly and peak streamflow forecasting in the Gilgit River Basin. The models utilized were LSTM, BiLSTM, GRU, CNN, and their hybrid combinations (CNN-LSTM, CNN-BiLSTM, CNN-GRU, and CNN-BiGRU). Our research measured the model’s accuracy through root mean square error (RMSE), mean absolute error (MAE), Nash–Sutcliffe efficiency (NSE), and the coefficient of determination (R2). The findings indicated that the hybrid models, especially CNN-BiGRU and CNN-BiLSTM, achieved much better performance than traditional models like LSTM and GRU. For instance, CNN-BiGRU achieved the lowest RMSE (71.6 in training and 95.7 in testing) and the highest R2 (0.962 in training and 0.929 in testing). A novel aspect of this research was the integration of MODIS-derived snow-covered area (SCA) data, which enhanced model accuracy substantially. When SCA data were included, the CNN-BiLSTM model’s RMSE improved from 83.6 to 71.6 during training and from 108.6 to 95.7 during testing. In peak streamflow prediction, CNN-BiGRU outperformed other models with the lowest absolute error (108.4), followed by CNN-BiLSTM (144.1). This study’s results reinforce the notion that combining CNN’s spatial feature extraction capabilities with the temporal dependencies captured by LSTM or GRU significantly enhances model accuracy. The demonstrated improvements in prediction accuracy, especially for extreme events, highlight the potential for these models to support more informed decision-making in flood risk management and water allocation.