The Sacramento-San Joaquin Delta in California was an historic, vast inland freshwater wetland, where organic soils almost 20 meters deep formed over the last several millennia as the land surface elevation of marshes kept pace with sea level rise. A system of levees and pumps were installed in the late 1800s and early 1900s to drain the land for agricultural use. Since then, land surface has subsided more than 7 meters below sea level in some areas as organic soils have been lost to aerobic decomposition. As land surface elevations decrease, costs for levee maintenance and repair increase, as do the risks of flooding. Wetland restoration can be a way to mitigate subsidence by re-creating the environment in which the organic soils developed. A preliminary study of the effect of hydrologic regime on carbon cycling conducted on Twitchell Island during the mid-1990s showed that continuous, shallow flooding allowing for the growth of emergent marsh vegetation re-created a wetland environment where carbon preservation occurred. Under these conditions annual plant biomass carbon inputs were high, and microbial decomposition was reduced. Based on this preliminary study, the U.S. Geological Survey re-established permanently flooded wetlands in fall 1997, with shallow water depths of 25 and 55 centimeters, to investigate the potential to reverse subsidence of delta islands by preserving and accumulating organic substrates over time. Ten years after flooding, elevation gains from organic matter accumulation in areas of emergent marsh vegetation ranged from almost 30 to 60 centimeters, with average annual carbon storage rates approximating 1 kg/m2, while areas without emergent vegetation cover showed no significant change in elevation. Differences in accretion rates within areas of emergent marsh vegetation appeared to result from temporal and spatial variability in hydrologic factors and decomposition rates in the wetlands rather than variability in primary production. Decomposition rates were related to differences in hydrologic conditions, including water temperature, pH, dissolved oxygen concentration, and availability of alternate electron acceptors. The study showed that marsh re-establishment with permanent, low energy, shallow flooding can limit oxidation of organic soils, thus, effectively turning subsiding land from atmospheric carbon sources to carbon sinks, and at the same time reducing flood vulnerability.