Salt marshes are research hotspots of the carbon cycle in coastal zones because large amounts of atmospheric carbon dioxide is fixed by salt marshes vegetation and stored in its biomass and soil. Dissolved organic carbon (DOC) in submarine groundwater (well water and pore water) in salt marshes plays an important role in advective exchange between the salt marshes and coastal waters. However, the molecular characteristics of DOC in salt marsh groundwater are poorly understood because of the complex DOC structures and hydrodynamic process. In this study, fluorescent components and refractory DOC (RDOC) in submarine groundwater from a salt marsh (Chongming Island, China) and adjacent coastal water were characterized by fluorescence spectroscopy and nuclear magnetic resonance spectroscopy. The fluorescent components identified by parallel factor analysis indicated that humic-like substances dominated the chromophoric dissolved organic matter in the submarine groundwater. The chromophoric dissolved organic matter and dissolved organic matter in the submarine groundwater had non-conservative behaviors because of additions from terrestrial humic substances. The nuclear magnetic resonance spectra indicated that bioactive substances (carbohydrates) contributed only 13.2％–14.8％ of the dissolved organic matter in the submarine groundwater but carboxyl-rich alicyclic molecules (CRAMs), the main components of RDOC, contributed 64.5％ of the dissolved organic matter. Carbohydrates and CRAMs contributed 16.4％ and 61.7％ of the dissolved organic matter in the coastal water, similar to the contributions for submarine groundwater. The DOC concentration in submarine groundwater was 386±294 μmol/L, which was significantly higher than that in coastal water (91±19 μmol/L). The high DOC concentrations and >60％ relative RDOC content suggested that submarine groundwater may be an important source of RDOC to coastal seawater. This information will be helpful for estimating the climate effects of salt marsh blue carbon.