South Carolina coastal and inland wetlands are continentally important to resident, migrating, and wintering dabbling ducks (Anatini), diving and sea ducks (Aythini, Mergini, Oxyurini), pelagic waterbirds (Anhingidae, Laridae, Pelicanidae, and Phalcrocoracidae), and wading birds (Ardeidaie, Ciconiidae, Threskiornithidae). Our goal was to model wetland selection of these waterbird guilds in South Carolina during autumn–winter to determine habitat preferences and guide wetland conservation and restoration amid sea‐level rise and other coastal pressures. We conducted aerial surveys and recorded waterbird occurrence and relative abundance in winters 2017–2019. We modeled waterbird–habitat relationships relative to managed and unmanaged coastal and inland wetlands, legally protected conservation lands (e.g. federal, state, and private easements), and habitat diversity. Waterbirds selected a variety of wetlands emphasizing the importance of wetland diversity within habitat complexes. However, only managed tidal impoundments (MTIs) and protected conservation lands were selected across all waterbird guilds. Results suggest these are contemporary keystone habitats for promoting wintering waterbird abundance and diversity in South Carolina and other South Atlantic coastal regions. To compensate for future coastal wetland loss while facilitating the current and future needs of migrating and wintering waterbirds, we recommend: (1) identification and continued management of MTIs resilient to sea‐level rise; (2) strategic planning and partnerships for land acquisition and legal protections inland; and (3) land protection networks between extant coastal and inland sites designated for future construction and emigration of decommissioned MTIs. Stakeholder and partner engagement is paramount to prioritize resource allocation for the restoration, construction, and decommissioning of coastal and inland wetlands.