In this study, according to the reference setting based on the runoff video of 9:00 where the highest water level of 3.94 m has been recorded during the runoff of Cheon-mi Stream in Jeju Island by the attack of Typhoon no. 16 Sanba on September 17th, 2012, the error rate of long-distance and short-distance velocimetry and real-distance change rate by input error have been calculated and the input range value of reference point by stream has been suggested. In the reference setting process, if a long-distance reference point input error occurs, the real-distance change rate of 0.35 m in the x-axis direction and 1.35 m in y-axis direction is incurred by the subtle input error of 2~11 pixels, and if a short-distance reference point input error occurs, the real-distance change rate of 0.02 m in the x-axis direction and 0.81 m in y-axis direction is incurred by the subtle input error of 1~11 pixels. According to the long-distance reference point setting variable, the velocity error rate showed the range of fluctuation of at least 14.36% to at most 76.06%, and when calculating flux, it showed a great range of fluctuation of at least 20.48% to at most 78.81%.