Studies have investigated the role of litter type on soil organic nitrogen (SON) mineralization and the resulting chemical composition in aerobic soils; however, the role of anaerobic conditions have been limitedly explored. We determined the SON chemical composition and N mineralization rate with depth of two different vegetation types (emergent aquatic vegetation, EAV and submerged aquatic vegetation, SAV) and prevailing flooded soil conditions in a subtropical treatment wetland. The treatment wetland provided similar water quality and climate conditions across the vegetation types. Three soil depths were sampled, the surficial floc, recently accreted soil, and soil present before constructing the treatment wetland. The surficial floc material created from emergent plants exhibited a mean total carbon (TC) and total N (TN) of 364 g C kg−1 and 27 g N kg−1 vs 185 g C kg−1and 12 g N kg−1 for submerged plants. Despite these differences, there were no significant differences in the proportion of N that was soil organic nitrogen (SON). Mean extractable ammonium was lower (95 mg N kg−1) in SAV systems and may be due to increased pH (~9) during the day compared to EAV systems (207 mg N kg−1). For the chemical composition, the N-associated aromatics comprised 4.8% of the SON in SAV areas compared with just 1.6% for EAV, which suggests an increased SON recalcitrance in SAV created floc. The difference in EAV and SAV chemical composition may be important for the long-term storage of SON and future studies should focus on additional environmental factors that favor the formation of stable recalcitrant SON.