Estuaries occupy the boundaries between terrestrial and marine systems. Like upland soils, the soils of estuaries support plant growth, are susceptible to erosion and degradation of soil quality, and provide the physical and chemical resources needed for ecosystem growth and sustainability. In recognition of their importance to the health of coastal habitats, US soil scientists have begun to investigate the genesis and morphology of the soils in estuaries and near shore coastal environments. Several of the recent studies investigating estuary soils have been completed at the University of Maine. The research has included investigations of subaqueous soil-landform relationships, quantification of soil organic matter storage, and identification of organic carbon sources using stable isotope biogeochemistry. As with terrestrial soils, estuarine subaqueous soils store larger amounts of carbon than is present in the biomass of the ecosystems they support. In the top meter of soils in Maine's shallow estuaries, organic carbon storage is equivalent to total carbon storage in New England's moderately well-drained upland forested soils. In contrast to upland soils where carbon contents decrease exponentially with increasing soil depths, organic carbon contents in these estuarine soils are relatively constant to depths up to and greater than five meters. A more comprehensive quantification of organic carbon storage in these coastal systems may even reduce the quantity of carbon ‘missing' from global carbon storage estimates. Stable carbon isotope data identify that the majority of the organic carbon stored in these estuary soils was fixed by estuary biota. The terrestrial organic matter present is mostly in the soils at the edges which have experienced inundation and burial as a result of rising sea level. With increasing distance toward the estuary channel, the relative content of terrestrial organic matter decreases. These results challenge the widely held belief that the organic carbon stored in estuarine systems is primarily transported from the surrounding watershed via surface water.