One of the many goals of wetland restoration is to promote the long-term storage of carbon (C) in the terrestrial biosphere. Unfortunately, soil C reservoirs in restored wetlands are slow to accumulate even after hydrology and plant communities are reestablished. Oftentimes wetland restoration changes the soil matrix and thus can dramatically alter how soil C is stored and processed. Our research investigated whether soil organic matter (SOM) preservation theories derived from studies in non-wetland soil systems can be extended to wetland soils. We examined C associated with water-stable soil aggregates, minerals, and metal oxides within habitats of one natural and one restored tidal freshwater wetland. This study revealed that a majority of the soil C in the natural site was associated with large macroaggregates (> 2000 μm), and soils from the restored site stored more C in small macroaggregates (> 250 to < 2000 μm). Despite these different associations, the chemical composition of SOM followed similar patterns across each aggregate-size class. Results from the sequential extraction procedure suggest organo-metal oxide complexes do not contribute to C stabilization in these habitats. This research is one of the few studies that have examined C stabilization related to soil structure in wetland soils. Our results suggest soil aggregate formation may be an important mechanism driving C stabilization, and that disruption to macroaggregates may limit C accumulation in restored wetlands. Additional empirical research and long-term field monitoring are needed to confirm linkages between aggregate-C stabilization and accumulation in wetland soils.