An agricultural ditch in headwater of Jinjin River, located at a small watershed in Changsha county, was selected as the study area, changes and losses of nitrogen, phosphorus in ditches and effects of ecological interception from rainfall runoff were analyzed. The results showed that the pollutants concentration and rainfall runoff increased gradually at their highest in preliminary stage of rainfall，however, they decreased gradually after the rainfall.The highest total nitrogen and total phosphorus content reached up to 4.67 mg/L and 0.38 mg/L during raining time respectively, ammonium and nitrate were the predominant forms. The transportation content of total nitrogen and total phosphorus increased at first, and then declined by time, the total nitrogen and total phosphorus content appeared to their maximum at the third days and the second days after the rainfall respectively, and they gradually decreased by time. The ecological interception capacity in ditches of Acorus calamus L. and Zizania latifolia was obviously higher than that of natural purification sections, which indicated that plant interception and assimilation were vital to decrease the nitrogen and phosphorus. The total assimilated nitrogen and phosphorus amounts were 26.90 and 2.34 g/m2 respectively during the rainy season (between April and June) in ditches.The results could provide references for agricultural non point pollution control at river basin scale.