This study demonstrates an application of uncertainty analysis in evaluating methods of discharge measurement including: the velocity-area, rating curve and efficient methods based on the probabilistic velocity distribution equation. The measurement of river discharge plays a large part in the distribution of water resources. The conventional methods of discharge measurement are costly, time-consuming, and dangerous. Therefore the efficient method of discharge measurement which bases on the relationship between maximum and mean velocities being constant was employed to justify its alternative for the conventional methods: velocity-area and rating curve methods. Distribution test was applied to investigate the statistical properties of the uncertainties involved in the three methods of discharge measurement. Latin hypercube sampling (LHS) method was employed accordingly to assess the discharge features of the three methods of discharge measurement. The main purpose of this study is to quantify the uncertainty involved in several discharge measurement methods and justify the availability and reliability of using the efficient method as an alternative of the conventional methods. Results show that the correlation analysis also validates that the efficient method is a more reliable method than the rating curve method to yield accurate discharge measurements. Moreover, it also yielded comparably accurate measurements as those by the velocity-area method.