The present study was conducted to re-estimate the factors needed for the velocity-area method previously provided by ISO through precise actual scale experiments in order to verify the appropriateness of the errors of the individual factors presented by ISO 748 and ISO 1088. For this, a steady-state flow of a flow velocity of approximately 1 m/s, 7 m wide, and 1 m deep, was maintained in the mild slope channel located at the River Experiment Center (Andong) of the Korea Institute of Construction Technology. Under this condition, the objective was to measure the flow velocity very precisely with respect to the space by using a micro-ADV having a high accuracy of flow velocity measurement. The water depth was precisely measured before the generation of the flow by using Total Station. The ISO regulations and the results of the present experiment were applied to three different conditions. The uncertainty assessed by applying the results of the present experiment exceeded twice that of the uncertainty estimated by applying the uncertainty factors provided by ISO. The uncertainty of the lateral gap between measurement lines and the number of measurement points in the depth direction was dependent on the scale of rivers. However, ISO may have presented the uncertainty factors analyzed from the data obtained from a wide range of river scales. Therefore, the discharge estimated by the velocity-area method may be dependent on the scale of rivers. The errors of the individual factors of the velocity-area method derived from the present study may be applied to the estimation of the uncertainty of the discharge calculated by the velocity-area method in small rivers.