Abstract: Uncertainty of discharge measurement is often estimated by error tests or empirical and laboratory studies. However, those methods have limitations such as heavy workload and inaccuracy. A method named interpolated variance estimator, which is based on statistical techniques and on-site observations to estimate uncertainty in discharge measurement, is introduced and testified. Measured data at three stations namely Baihe, Xiangyang and Shayang along Hanjiang are analyzed. Besides, Monte Carlo test at Baihe Station is developed to investigate the difference between real error and uncertainty calculated by interpolated variance estimator. The results show that interpolated variance estimator can indicate very well the relationship between uncertainty in discharge measurement and water level. The correlation coefficient of uncertainty and real error derived in the Monte Carlo test is 0.64, and Spearman coefficient of uncertainty and water level is 0.79. Also, uncertainty for high and middle water levels is credible but is overestimated for low water level. These results illustrate that interpolated variance estimator, as a sound statistical method, can be recommended for use in broad applications.