The present study describes an automated system to measure the river flow velocity. A combination of the camera‐tracking system and the Proportional/Integral/Derivative (PID) control could enable the boat‐type robot to remain in position against the mainstream; this results in reasonable evaluation of the mean velocity by a duty ratio which corresponds to rotation speed of the screw propeller. A laser range finder module was installed to measure the local water depth. Reliable laboratory experiments with the prototype boat robot and electromagnetic velocimetry were conducted to obtain a calibration curve that connects the duty ratio and mean current velocity. The remaining accuracy in the target point was also examined quantitatively. The fluctuation in the spanwise direction is within half of the robot length. It was therefore found that the robot remains well within the target region. We used two‐dimensional navigation tests to guarantee that the prototype moved smoothly to the target points and successfully measured the streamwise velocity profiles across the mainstream. Moreover, the present robot was found to move successfully not only in the laboratory flume but also in a small natural river. The robot could move smoothly from the starting point near the operator's site toward the target point where the velocity is measured, and it could evaluate the cross‐sectional discharge.