This study assessed the efficacy of improving the accuracy of reservoir water level prediction models by employing automated machine learning models and efficient cross-validation methods for time-series data. Considering the inherent complexity and non-linearity of time-series data related to reservoir water levels, we proposed an optimized approach for model selection and training. The performance of twelve models was evaluated for the Obong Reservoir in Gangneung, Gangwon Province, using the TPOT (Tree-based Pipeline Optimization Tool) and four cross-validation methods, which led to the determination of the optimal pipeline model. The pipeline model consisting of Extra Tree, Stacking Ridge Regression, and Simple Ridge Regression showed outstanding predictive performance for both training and test data, with an R² (Coefficient of determination) and NSE (Nash-Sutcliffe Efficiency) exceeding 0.93. On the other hand, for predictions of water levels 12 hours later, the pipeline model selected through time-series split cross-validation accurately captured the change pattern of time-series water level data during the test period, with an NSE exceeding 0.99. The methodology proposed in this study is expected to greatly contribute to the efficient generation of reservoir water level predictions in regions with high rainfall variability.