River runoff is not only a crucial part of the global water cycle, but it is also an important source for hydropower and an essential element of water balance. This study presents a system-theory-based model for river runoff forecasting taking the Hailiutu River as a case study. The forecasting model, designed for the Hailiutu watershed, was calibrated and verified by long-term precipitation observation data and groundwater exploitation data from the study area. Additionally, frequency analysis, taken as an optimization technique, was applied to improve prediction accuracy. Following model optimization, the overall relative prediction errors are below 10%. The system-theory-based prediction model is applicable to river runoff forecasting, and following optimization by frequency analysis, the prediction error is acceptable.