A watershed runoff prediction system, method, and storage medium recording computer readable programs for executing the method are disclosed. The watershed runoff prediction system includes a data input section, a rainfall calculation section, an evaporation calculation section, an actual rainfall calculation section, a runoff calculation section, and a runoff output section. The data input unit receives preset input data including precipitation, temperature, and potential evaporation amount for the target watershed, and the rainfall calculation unit calculates rainfall using the input data, and the evaporation amount calculation unit uses the rainfall amount and the preset soil moisture storage amount. Calculate the amount of available water, calculate the amount of evapotranspiration using the amount of available water, calculate the actual amount of rainfall using the amount of rainfall and evapotranspiration, and calculate the amount of discharge from the base using the amount of soil moisture and the amount of actual rainfall. Calculate and sum the base runoff and surface runoff to calculate the total runoff, and the runoff output outputs the runoff.
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