Abstract: In the discharge measurements of the river, the acoustic Doppler current profiler (ADCP) generally adopts the bottom tracking mode (i.e. taking the river bottom as the reference system) to obtain the discharge velocity and cross-sectional area and then to obtain the discharge of the current watershed basin. But, when there is a large amount of sediments in the river, the "moving bottom" appears, therefore the bottom tracking velocity lacks the downstream component to cause the bottom tracking trajectory shifting upstream, and so the bottom tracking velocity is small, resulting in a small flow. In this paper, the principle of moving bottom is analyzed and the "loop method" in the dynamic bottom measurements is studied, and then a measurement method of average dynamic bottom velocity based on global positioning system fix data (GGA) mode and two moving bottom flow compensation methods are proposed. Through the analysis and verification of the measured data, the results show that the moving bottom velocity measurement method and the moving bottom flow compensation method proposed in this paper are significantly effective for "moving bottom" detection and compensation.