Groundwater storage is vital for managing water resources, especially as global water scarcity intensifies. Estimating groundwater levels regionally is challenging due to natural heterogeneity. We employed a large groundwater observation sample, along with Global Land Data Assimilation System (GLDAS) and Gravity Recovery and Climate Experiments (GRACE) datasets, to develop a random forest model for predicting groundwater levels in China’s Yellow River Basin. The model showed robustness, achieving an R² of 0.95 in calibration and an R² of 0.91 ± 0.009 in 10-fold cross-validation with 100 repetitions. Temporal predictability was lower, with an R² of 0.72 for April–May 2023; however, the temporal prediction is preliminary and limited by the short validation period (April–May 2023), which should be interpreted with caution. Spatial maps revealed significant seasonal declines in fall and winter, particularly in the middle and lower reaches. This study highlights the potential of machine learning with extensive observations to estimate regional groundwater levels and supports groundwater analysis with robust data.