Coastal freshwater forested wetlands are rapidly transitioning from forest to marsh, leaving behind many standing dead trees (snags) in areas often called ‘ghost forests’. Snags can act as conduits for soil produced greenhouse gases (GHG) and can also be sources as they decompose. Thus, snags have the potential to contribute GHGs to the atmosphere, but emissions are not well understood. We assessed GHG emissions (carbon dioxide—CO2, methane—CH4, and nitrous oxide—N2O) from snags and soils in five ghost forests along a salinity gradient on the coast of North Carolina, USA. Mean (± SE) soil GHG fluxes (416 ± 44 mg CO2 m−2 h−1, 5.9 ± 1.9 mg CH4 m−2 h−1, and 0.1 ± 0.06 mg N2O m−2 h−1) were ~ 4 times greater than mean snag GHGs (116 ± 15 mg CO2 m−2 h−1, 0.3 ± 0.09 mg CH4 m−2 h−1, and 0.04 ± 0.009 mg N2O m−2 h−1). Hydrological conditions and salinity influenced soil GHG fluxes between the two field campaigns, but snags were less predictable and more variable. Snag and soil CO2/N2O fluxes were influenced by similar environmental parameters. The drivers for soil and snag CH4 however, were often not the same and at times oppositely correlated. Our results illustrate the need to further research into the drivers and importance of GHG emissions from snags, and the need to include tree stems into ecosystem GHG research.