The distribution of carbon (C) within a salt marsh may vary among vegetation zones depending on production and decomposition dynamics and organic and mineral depositional history. We examined spatial and temporal variation of plant and soil C pools within a salt marsh fringing a coastal lagoon along the mid-Atlantic coast of the U.S. The total plant C pool increased from high marsh shrub to low marsh grass dominated areas. Much of the spatial variation in plant C pool was due to fine roots and small organic matter (dlm) that could not be identified by species, which averaged 2398 g C m−2 in Spartina patens-dominated, 2215 g C m−2 in Spartina alterniflora-dominated, and 676 g C m−2 in Juncus roemerianus-dominated areas. Belowground C pool loss was 36% less for S. patens than S. alterniflora and was similar between S. alterniflora and J. roemerianus. Accretion and C accumulation rates were greater in the S. alterniflora-dominated stand than in the J. roemerianus-dominated stand. Our results suggest that landward migration onto terrestrial soils can lead to an estimated 80% increase in belowground plant C composed primarily of fine roots and dlm and 36–70% increase in soil carbon between 15 and 30 cm depths.