Aerial surveys integrating probability-based sample designs have been implemented successfully to estimate relative abundance of wintering ducks in Arkansas, Louisiana, Mississippi, and Missouri, but these approaches have not been evaluated in the Atlantic Flyway except for American black ducks (Anas rubripes) along the Atlantic coast. Furthermore, these surveys have not been used to index abundance of other nonbreeding waterbirds. Given elimination or reduction of resources allocated to the Midwinter Waterfowl Survey in the Atlantic Flyway and elsewhere, the South Carolina Department of Natural Resources (SCDNR) expressed a need for reliable surveys to monitor waterfowl and other waterbirds during autumn through winter. We designed stratified aerial strip-transect surveys to estimate population indices for migrating and wintering dabbling ducks (Anatini), diving ducks (Aythini, Mergini, Oxyurini), pelagic and piscivorous waterbirds (Anhingidae, Laridae, Pelicanidae, Phalacrocoracidae), and wading birds (Ardeidae, Ciconiidae, Threskiornithidae) in coastal and inland regions of South Carolina during autumn-winter 2017–2019. We used unequal probability random sampling to estimate population indices with deemed adequate precision (i.e., coefficient of variation [CV] ≤ 20%) and estimated theoretical survey efforts needed to achieve desired precision for future aerial surveys. Indices met our goal for precision in September and January 2018 for wading birds, in February and November 2018 for pelagic waterbirds, and in February 2018 for diving ducks, but never for other ducks during South Carolina waterfowl hunting season. We detected peak abundance of dabbling and diving ducks in January and wading birds and wood storks (Mycteria americana) in September. We estimated ~2.5 times greater survey effort was needed across waterbird taxa than was expended to achieve a CV=20%. We also used survey data to depict spatiotemporal variation in waterbird distributions across the study area. Our surveys are applicable for the SCDNR and other agencies seeking to monitor autumn-winter waterbird populations. Although survey refinements are necessary to increase precision in South Carolina, our waterbird indices are useful to assess population trends through time, guide habitat management and restoration efforts, refine local harvest regulations, inform law enforcement to detected illicit activities (e.g., baiting), and monitor possible shifting waterbird distributions in response to land-use and climate change.