Aim of this research was study effect of flood on soil carbon and nitrogen sequestration the soil of the habitat of three plant species Tamarix sp., Halostachys belangeriana and Suaeda  fruticosa Sistan region. To do this research first by survey satellite images, the areas were found that watering and no watering (control treatments) from Afghanistan floods. Then select the introductory treatments, 48 soil samples with five repetitions were collected randomly at 0-30 centimeter soil depth and analyzed Organic carbon, nitrogen, sequestered soil carbon and sequestered soil nitrogen from the three flood and control sites. In order to the compare carbon sequestration and nitrogen between treatments and control treatment using the one-way analysis of variance. Data shows that there were significant difference between soil organic carbon percentage and nitrogen in 0.05 levels. The Pearson correlation coefficient between data shows that the maximum amount of correlation of organic carbon and nitrogen was with organic matter (96%) which was significant at the 99% probability level. The result also shows that the above parameter has 99% negative correlation with soil apparent specific weight. Average comparison mean of carbon sequestration and nitrogen of soil shows that the maximum carbon sequestration and nitrogen were in Tamarix forest with 21.89 and 2.43 ton/ha, respectively. This is equivalent to 80.33 and 8.01 ton of carbon dioxide and air nitrogen dioxide in soil which 2.2 and 2.5 times of carbon sequestration and nitrogen of control treatment (9.76 and 0.97 ton/ha). Environmental economic value of carbon sequestration and nitrogen in floodplain is equivalent $ 300 and 85 billion per hectare, respectively. It is recommended to prevent further effects of climate change on the dry and sensitive ecosystem of Sistan region, increase vegetation through the flow of incoming floods from Afghanistan to eroded areas and seedlings should also be planted in these areas.