Carbon storage was compared between impounded and naturally tidal freshwater marshes along the Lower Waccamaw River in South Carolina, USA. Soil cores were collected in (1) naturally tidal, (2) moist soil (impounded, seasonally drained since ~1970), and (3) deeply flooded “treatments” (impounded, flooded to ~90 cm since ~2002). Cores were analyzed for % organic carbon, % total carbon, bulk density, and 210Pb and 137Cs for dating purposes. Carbon sequestration rates ranged from 25 to 200 g C m−2 yr−1 (moist soil), 80–435 g C m−2 yr−1 (naturally tidal), and 100–250 g C m−2 yr−1 (deeply flooded). The moist soil and naturally tidal treatments were compared over a period of 40 years. The naturally tidal treatment had significantly higher carbon storage (mean = 219 g C m−2 yr−1 vs. mean = 91 g C m−2 yr−1) and four times the vertical accretion rate (mean = 0.84 cm yr−1 vs. mean = 0.21 cm yr−1) of the moist soil treatment. The results strongly suggest that the long drainage period in moist soil management limits carbon storage over time. Managers across the National Wildlife Refuge system have an opportunity to increase carbon storage by minimizing drainage in impoundments as much as practicable.