River discharge is crucial to water resources development and ecological protection. How-ever, in some arid areas of northwest China, it is still difficult to measure discharge accurately. In this study, unmanned aerial vehicle (UAV) imagery has been used to estimate river discharge at two river sections in the upper reaches of the Shiyang River in the eastern part of the Qilian Mountains based on the Manning formula. The estimated discharges at those two sections are 1.16 m3/s and 3.11 m3/s, respectively. Taking the discharges measured by an acoustic Doppler current profiler (ADCP) as the reference, the relative error of the estimates is below 5%, which is accurate enough for water resources management in mountain basin regions. Multiple high‐resolution satellite images were also used to calculate water discharges at the two sections, which were in good agreement with the discharges estimated from UAVs. This study demonstrates the feasibility of using UAVs to estimate river discharge, which is of great significance for future regional‐scale water resource assessments. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.