Depends entirely on what you want as an output. If you just want a peak flow rough estimate, you can use the rational method. Then you only need your drainage area (watershed area calculated in GIS), the runoff coefficient, and rainfall intensity. If you want anything much more complex, you will need to use a hydrologic modeling software (HEC-HMS is a common free one). GIS can help you get much of the input needed for these models including basins, streams, curve numbers, and time of concentration, but the modeling software will require other inputs such as your storm hydrographs and any gauge locations for calibration.
