Annual dynamics of CO2, CH4, N2O emissions from freshwater marshes and affected by nitrogen fertilization were studied in situ in Sanjiang Plain of Northeast China from June 2002 to December 2004, using the static opaque chamber-GC techniques. The results showed that there was significant seasonal and annual variation in the CO2, CH4 and N2O emissions. The ecosystem emission of CO2 reached a maximum of 779.33- 965.40 mg x (mxh)(-1) in July and August, CH4 reached a maximum of 19.19-30.52 mg x (mxh)(-1) in August, N2O reached a maximum of 0.072-0.15 mgx (mxh)(-1) in May and September, respectively. While the minimum of the CO2, CH4, N2O emission was 2.36-18.73 mg x (mxh)(-1), - 0.35 - 0.59 mg x (mxh)(-1), - 0.032- 0.009 mg (mxh)(-1), respectively, which occurs in winter. The freshwater marsh was the sink of N2O in winter. Temperature was a primary factor, controlling greenhouse gas seasonal emissions in freshwater marshes; while the precipitation and floodwater depth were the dominating influencing factors, affecting the greenhouse gas annual variations. Especially, the influence of precipitation on CH4 emissions was more obvious, comparing with the CO2 and N20 emissions. And the summer higher CH4 emission was mainly induced by the ice and snow thawing water in winter. Respiration of the ecosystem and CH4 emission were exponentially dependent on soil temperature of 5cm depth, while the N2O emission was not related to the soil temperature and water depth. The greenhouse gas (CO2, CH4, N2O) emissions were significantly influenced by nitrogen fertilization in Sanjiang Plain. The CO2, CH4, N2O flux of fertilization increased 34% , 145% , 110% , respectively, comparing to the control treatment.