River slopes can be changed due to an extreme event, e.g., a large-scale earthquake. This can uplift a riverbed greatly and thereby change the behavior of the river flow into a free or submerged overfall. Corresponding damage, including extreme erosion, on bridge piers located in the river can take place due to the aforementioned flow conditions. A reconstructed bridge pier in the same location would also experience a similar impact if the flow condition is not changed. It is important to identify these phenomena and research the mechanism in the interaction between overfall types and scour at bridge piers. Therefore, this paper is aimed at studying a mechanism of free and submerged overfall flow impacts on bridge piers with different distances by a series of moving-bed experiments. The experiment results showed clearly that bridge pier protection requires attention particularly when the pier is located in the maximum scour hole induced by the submerged overfall due to the z directional flow eddies. In many other cases, such as when the location of the bridge pier was at the upstream slope of a scour hole induced by a flow drop, a deposition mound could be observed at the back of the pier. This indicates that, while a pier is at this location, an additional protection takes place on the bridge pier.