In the middle reaches of gravel-bed rivers, the formation of alternate or linguoid bars provides a diverse microhabitat for many kinds of creatures, much as with riffle pools and dry riverbed areas. The riverbed configuration, however, is completely altered by river-crossing structures, such as weirs or drop structures, installed in a river channel. In this study, both a large river and a small stream that have many river-crossing structures were targeted, and the characteristic feature of the topography in a river channel was investigated. Consequently, there was clarification that a similar pattern of topography was created in both rivers. The elevation gap between the bank and the riverbed was largest just downstream of a river-crossing structure but decreased in the flow direction and disappeared upstream of the next structure. Contrastingly, the width of the low-flow channel was narrowest just downstream of a river-crossing structure and gradually increased in the flow direction. The implication was that the longitudinal profile of the bank was determined by significant past floods and the low-flow channel was gradually created by small floods afterwards. Based on these results, we conclude that a change of river-crossing structure height is effective to manage the floodplain for habitat control, and the installation of large boulder is also effective to restore the low-flow channel.