Compound open canal junctions are of considerable importance in many engineering applications. This paper presents the details of the experimental procedure and the transitional flow characteristics over a partially rough bed in a right‐angled canal junction. To record the instantaneous flow velocity, a 3D downward‐facing acoustic Doppler velocimeter is used. A simplified mathematical model is employed to give a reasonable prediction of experimental results of a small portion of the data recorded. The hydraulics of flow at the canal junction, wherein the flow regime changes from subcritical to supercritical, is observed. The experimental results are presented in light of a dimensionless framework. The results reveal that the physical model describes the flow features well when there are changes in flow state from sub‐ to supercritical. Results of the present observation are compared with the available literature data. Being the first real study of transitional flow, the present work has provided valuable basic information about fundamental aspects of the hydrodynamics model. Copyright © 2016 John Wiley & Sons, Ltd.