Seasonally flooded, freshwater cypress-tupelo wetlands, dominated by baldcypress (Taxodium distictum), water tupelo (Nyssaaquatica), and swamp tupelo (Nyssa sylvatica var. biflora) are commonly found in coastal regions of the southeastern United States. These wetlands are threatened due to climate change, sea level rise, and coastal urban development. Understanding the natural biogeochemical cycles of nutrients in these forested wetlands as ecosystems services such as carbon sequestration and nitrogen processing can provide important benchmarks to guide conservation plans and restoration goals. In this study, surface water and soil pore water samples were collected weekly from a cypress-tupelo wetland near Winyah Bay, South Carolina and analyzed for dissolved organic carbon (DOC), dissolved organic nitrogen (DON), inorganic nitrogen, and phosphate during its flooding period between October 2010 and May 2011. DOC was further characterized by specific ultra-violet absorbance at 254 nm, spectral slope ratio (SR) (ratio of two spectral slopes between 275–295 nm and 350–400 nm), E2/E3 ratio (ratio between A254 and A365), and fluorescence excitation-emission matrix. In addition, litterfall was collected on a monthly basis for a year while the biomass of the detritus layer (i.e., decomposed duff lying on the wetland floor) was determined before and after the flooding period. Results of the field study showed that concentrations of DOC, DON, NH4+–N, and (NO2− + NO3−)–N in the surface water were generally higher during the fall, or peak litterfall season (October to December), than in the spring season (March to May). Highest concentrations of 54.8, 1.48, 0.270, and 0.0205 mg L−1, for DOC, DON, NH4+–N, and (NO2− + NO3−)–N respectively, in surface waters were recorded during October. Lower SUVA, but higher SR and E2/E3 ratios of DOC, were observed at the end of the flooding season comparing to the initial flooding, suggesting the wetland system converts high aromatic and large DOC molecules into smaller and hydrophilic fractions possibly through photochemical oxidation. A similar trend was observed in soil pore water, but the pore water generally had greater and relatively stable concentrations of dissolved nutrients than surface water. No obvious temporal trend in phosphate concentration and total nitrogen to total phosphorus ratio (N:P) were found. Results of the laboratory extraction and mass balance calculation suggested fresh litter was a major source of DOC whereas decomposed duff was the source of dissolved nitrogen in surface water. In summary, the biogeochemistry of this isolated cypress-tupelo wetland is not only driven by the vegetation within the wetland system but also by hydrology and weather conditions such as groundwater table position, precipitation, and temperature.