Many waterbird species utilize a diversity of aquatic habitats; however, with increasing anthropogenic needs to manage water regimes there is global concern over impacts to waterbird populations. The federally threatened Piping Plover (Charadrius melodus; hereafter plovers) is a shorebird that breeds in three habitat types in the Prairie Pothole Region of North Dakota, South Dakota, and Canada: riverine sandbars; reservoir shorelines; and prairie wetlands. Water surface areas of these habitats fluctuate in response to wet-dry periods; decreasing water surface areas expose shorelines that plovers utilize for nesting. Climate varies across the region so when other habitats are unavailable for plover nesting because of flooding, prairie wetlands may periodically provide habitat. Over the last century, many of the wetlands used by plovers in the Prairie Pothole Region have been modified to receive water from consolidation drainage (drainage of smaller wetlands into another wetland), which could eliminate shoreline nesting habitat. We evaluated whether consolidation drainage and fuller wetlands have decreased plover presence in 32 wetlands historically used by plovers. We found that wetlands with more consolidation drainage in their catchment and wetlands that were fuller had a lower probability of plover presence. These results suggest that plovers could have historically used prairie wetlands during the breeding season but consolidation drainage and/or climate change have reduced available shoreline habitat for plovers through increased water levels. Prairie wetlands, outside of some alkali wetlands in the western portion of the region, are less studied as habitat for plovers when compared to river and reservoir shorelines. Our study suggests that these wetlands may have played a larger role in plover ecology than previously thought. Wetland restoration and conservation, through the restoration of natural hydrology, may be required to ensure that adequate habitat exists among the three habitat types in the face of existing or changing climate and to ensure long-term conservation.