The invention discloses a method and system for predicting short-term running water. The method comprises the steps of: S1, analyzing a running water law in a river basin and initializing data, wherein the analysis of the running water law in the river basin comprises analysis on relevance and characteristics of the river basin, analysis on running water sequence period and trend of the river basin, hydrologic year division, staging of reservoir regulation and selection of step-shaped typical year of the river basin; S2, establishing and calling a short-term running water prediction model; and S3, solving the short-term running water prediction model, verifying if the precision of the model is optimal, and outputting a short-term running water prediction result. According to the method and system for predicting the short-term running water, disclosed by the invention, the precision of prediction of the short-term running water can be improved.