Constructed wetlands used for the treatment of swine wastewater may potentially sequester significant amounts of carbon. In past studies, we evaluated the treatment efficiency of wastewater in a marsh–pond–marsh design wetland system. The functionality of this system was highly dependent on soil carbon content and organic matter turnover rate. To better understand system performance and carbon dynamics, we measured plant dry matter, decomposition rates and soil carbon fractions. Plant litter decomposition rate was 0.0052 g day−1 (±0.00119 g day−1) with an estimated half-life of 133 days. The detritus layer accumulated over the soil surface had much more humin than other C fractions. In marsh areas, soil C extracted with NaOH had four to six times higher amounts of humic acid, fulvic acid and humin than soil C extracted by cold and hot water, HCl/HF, and Na pyruvate. In the pond area, humic acid, fulvic acid and humin content were two to four times lower than in the marsh area. More soil C and N was found in the marsh area than in the pond area. These wetlands proved to be large sinks for stable C forms.