The economic operation of hydropower stations has the potential to increase water use efficiency. However, there are some challenges, such as the fixed and unchangeable flow characteristic curve of the hydraulic turbines, and the large number of variables in optimal load distribution, which limit the progress of research. In this paper, we propose a new optimal method of the economic operation of hydropower stations based on improved Long Short-Term Memory neural network (I-LSTM) and Random Forest (RF) algorithm. Firstly, in order to accurately estimate the water consumption, the LSTM model’s hyperparameters are optimized using improved particle swarm optimization, and the I-LSTM method is proposed to fit the flow characteristic curve of the hydraulic turbines. Secondly, the Random Forest machine learning algorithm is introduced to establish a load-distribution model with its powerful feature extraction and learning ability. To improve the accuracy of the load-distribution model, we use the K-means algorithm to cluster the historical data and optimize the parameters of the Random Forest model. A Hydropower Station in China is selected for a case study. It is shown that (1) the I-LSTM method fits the operating characteristics under various working conditions and actual operating characteristics of hydraulic turbines, ensuring that they are closest to the actual operating state; (2) the I-LSTM method is compared with Support Vector Machine (SVM), Extreme Learning Machine (ELM) and Long Short-Term Memory neural network (LSTM). The prediction results of SVM have a large error, but compared with ELM and LSTM, MSE is reduced by about 46% and 38% respectively. MAE is reduced by about 25% and 21%, respectively. RMSE is reduced by about 27% and 24%, respectively; (3) the RF algorithm performs better than the traditional dynamic programming algorithm in load distribution. With the passage of time and the increase in training samples, the prediction accuracy of the Random Forest model has steadily improved, which helps to achieve optimal operation of the units, reducing their average total water consumption by 1.24%. This study provides strong support for the application of intelligent low-consumption optimization strategies in hydropower fields, which can bring higher economic benefits and resource savings to renewable energy production.