We measured organic carbon input and content of soil in two wetland areas of Chongming Dongtan (Yangtze River Estuary) to evaluate variability in organic carbon accumulation capability in different wetland soils. Observed differences were investigated based on the microbial activity and environmental factors of the soil at the two sites. Results showed that the organic carbon content of wetland soil vegetated with Phragmites australis (site A) was markedly lower than that with P. australis and Spartina altemiflora (site B). Sites differences were due to higher microbial activity at site A, which led to higher soil respiration intensity and greater carbon outputs. This indicated that the capability of organic carbon accumulation of the site B soils was greater than at site A. In addition, petroleum pollution and soil salinity were different in the two wetland soils. After bio-remediation, the soil petroleum pollution at site B was reduced to a similar level of site A. However, the culturable microbial biomass and enzyme activity in the remediated soils were also lower than at site A. These results indicated that greater petroleum pollution at site B did not markedly inhibit soil microbial activity. Therefore, differences in vegetation type and soil salinity were the primary factors responsible for the variation in microbial activity, organic carbon output and organic carbon accumulation capability between site A and site B.