Energy use forecasting is crucial in balancing the electricity supply and demand to reduce the uncertainty inherent in the inter-basin water transfer project. Energy use prediction supports the reliable water-energy supply and encourages cost-effective operation by improving generation scheduling. The objectives are to develop subsequent monthly energy use predictive models for the Mokelumne River Aqueduct in California, US. Partial objectives are to (a) compare the model performance of a baseline model (multiple linear regression (MLR)) to three machine learning-based models (random forest (RF), deep neural network (DNN), support vector regression (SVR)), (b) compare the model performance of the whole system to three subsystems (conveyance, treatment, distribution), and (c) conduct sensitivity analysis. We simulate a total of 64 cases (4 algorithms (MLR, RF, DNN, SVR) x 4 systems (whole, conveyance, treatment, distribution) x 4 scenarios (different combinations of independent variables). We concluded that the three machine learning algorithms showed better model performance than the baseline model as they reflected non-linear energy use characteristics for water transfer systems. Among the three machine learning algorithms, DNN models yielded higher model performance than RF and SVR models. Subsystems performed better than the whole system as the models more closely reflected the unique energy use characteristics of the subsystems. The best case was having water supply (t), water supply (t-1), precipitation (t), temperature (t), and population (y) as independent variables. These models can help water and energy utility managers to understand energy performance better and enhance the energy efficiency of their water transfer systems.