In the mountain streams in Jeju Island, strong turbulence and roughness usually made it nearly impossible to utilize most of intrusive instrumentation for streamflow discharge measurements. Instead, a non-intrusive fixed electro-magnetic wave surface velocimetry (fixed EWSV: Kalesto) became alternatively popular in many representative streams to measure stream discharge seamlessly. Currently, Kalesto has shown noteworthy performance with little loss in flood discharge measurements and also has successfully provided discharge for every minute. However, Kalesto has been operated to regard its measured one-point velocity as the representative mean velocity for the given cross-section. Therefore, it could be highly possible to potentially encompass discharge measurements errors. In this study, we analyzed the difference between such Kalesto discharge measurements and other alternative concurrent discharge measurements such as Acoustic Doppler Current Profiler (ADCP) and mobile EWSV which were able to measure velocity in multi-points in the cross-section. Consequently, Kalesto discharge deviated from ADCP discharge in amount of 48% for relatively low flow, and more than 20% difference for high flow compared with mobile EWSV discharge measurements. These results indicated that the one-point velocity measured by Kalesto should be used as a cross-sectional mean velocity, rather it should be accounted for as an index-velocity in conjunction with directly measured cross-sectional mean velocity by using more reliable instrumentations. After inducing Kalesto Discharge Correction Coefficient (KDCC) that actually means relationship between index velocity and cross-sectional mean velocity, the corrected discharge from Kalesto was significantly improved. Therefore, we found that index velocity method should be applied to obtain better accuracy of discharge measurement in case of Kalesto operation.