Accurate prediction of water quality that is essential for effective lake management requires a comprehensive understanding of influential factors in the ’land-river-lake’ continuum. We develop a novel deep learning model employing a Long Short-Term Memory (LSTM) model for predicting water quality, and apply it for a large plateau lake, Lake Dianchi. The model comprises two stages: the first establishes a correlation between land and rivers by predicting nutrient loads, incorporating socioeconomic and meteorological features. The second establishes a correlation between feeding rivers and the lake by predicting nutrient concentrations, taking water quality, meteorological conditions, riverine import, and agricultural Non-Point Source (NPS) loads into consideration. Compared to single-stage deep learning models developed using classical methods, the two-stage model reduces Mean Absolute Percentage Error (MAPE), Mean Absolute Error (MAE), and Root Mean Square Error (RMSE), indicating enhanced prediction accuracy. Shapley Additive Explanation (SHAP) analysis is further employed to identify key contributing features. Precipitation emerges as the primary feature in the first stage, while in the second stage, disparities in the most contributing features for two zones of the lake are revealed due to dam isolation and water diversion projects. In the main zone, the primary predicting features are temperature and agricultural NPS features, while in the dam-isolated zone, Secchi depth is the key predictor, highlighting spatial–temporal variations in driving features. Our model contributes a novel deep learning framework and valuable insights for water quality management in large lakes, emphasizing the importance of considering the dynamic interplay of features or factors in the ’land-river-lake’ system.