During flood period, the bed load deposited behind a run-of-river dam on a mountain river could be carried over the dam crest by the flow which would intensify sediment transport. In this study, flume experiments are conducted to reveal the transport process of bed load from upstream to downstream after starting, advancing, and then over the top of a dam. This study analyzes the variation and mathematics of sediment transport parameters; describes the over-dam sediment transport model and its movement characteristics; and clarifies the natural relationship between sediment transport rule and riverbed morphology. In general, the findings of this study are:① The relationship between the volume of sediment transport and time can be expressed using a power function; ② The morphology of riverbed around the dam will stabilize, and form stable curved slope deposits in the upstream and downstream; ③ The over-dam transport modes of bed load are distinct under different flow intensities. For general flow intensities, sediment particles roll or slide on the curved slope surface of the upstream sediment body at the beginning. When they are close to the dam, they are carried over the dam crest by the flow and transported to the downstream. For higher flow intensities, the later over-dam transport mode could change significantly. Specifically, the periodic edge-wall vortex is the key driver of over-dam sediment transport.