Resumen: The world’s water ecosystems have been affected by various human activities. Artificial intelligence techniques, especially machine learning, have become an important tool for predicting the water quality of inland aquatic ecosystems. As an excellent biological indicator, chlorophyll-a was studied to determine the state of water quality in Lake Llanquihue, located in southern Chile. A 31-year time series (1989 to 2020) of data collected in situ was used to determine the evolution of limnological parameters at eight spaced stations covering all of the main points of the lake, and the year, month, day, and hour time intervals were selected. Using machine learning techniques, out of eight estimation algorithms that were applied with real data to estimate chlorophyll-a, three models showed better performance (XGBoost, LightGBM, and AdaBoost). The results for the best models show excellent performance, with a coefficient of determination between 0.81 and 0.99, a root-mean-square error of between 0.03 ug/L and 0.46 ug/L, and a mean bias error of between 0.01 and 0.27 ug/L. These models are scalable and applicable to other lake systems of interest that present similar conditions and can support decision making related to water resources.