The use of Acoustic Doppler current profilers (ADCP) for measuring discharge in streams with sediment transport was discussed. The studies show that the acoustic frequency of an ADCP in combination with the sediment transport characteristics in a river causes the ADCP bottom-tracking algorithms to detect a moving bottom. A moving bottom causes bottom-tracking-referenced water velocities and discharges to be biased low. The results also show that the use of differential global positioning system (DGPS) data allows accurate measurement of water velocities and discharges in such cases.