Determining the influences of anthropogenic perturbations on side channel dynamics in large rivers is important from both assessment and monitoring perspectives because side channels provide critical habitat to numerous aquatic species. Side channel extents are decreasing in large rivers worldwide. Although riprap and other linear structures have been shown to reduce side channel extents in large rivers, we hypothesized that small “anthropogenic plugs” (flow obstructions such as dikes or berms) across side channels modify whole-river geomorphology via accelerating side channel senescence. To test this hypothesis, we conducted a geospatial assessment, comparing digitized side channel areas from aerial photographs taken during the 1950s and 2001 along 512 km of the Yellowstone River floodplain. We identified longitudinal patterns of side channel recruitment (created/enlarged side channels) and side channel attrition (destroyed/senesced side channels) across n = 17 river sections within which channels were actively migrating. We related areal measures of recruitment and attrition to the density of anthropogenic side channel plugs across river sections. Consistent with our hypothesis, a positive spatial relationship existed between the density of anthropogenic plugs and side channel attrition, but no relationship existed between plug density and side channel recruitment. Our work highlights important linkages among side channel plugs and the persistence and restoration of side channels across floodplain landscapes. Specifically, management of small plugs represents a low-cost, high-benefit restoration opportunity to facilitate scouring flows in side channels to enable the persistence of these habitats over time.