Natural wetlands are critically important to global change because of their role in modulating atmospheric concentrations of CO2, CH4, and N2O. One 4-year continuous observation was conducted to examine the exchanges of CH4 and N2O between three wetland ecosystems and the atmosphere as well as the ecosystem respiration in the Sanjiang Plain in Northeastern China. From 2002 to 2005, the mean annual budgets of CH4 and N2O, and ecosystem respiration were 39.40 ± 6.99 g C m−2 yr−1, 0.124 ± 0.05 g N m−2 yr−1, and 513.55 ± 8.58 g C m−2 yr−1 for permanently inundated wetland; 4.36 ± 1.79 g C m−2 yr−1, 0.11 ± 0.12 g N m−2 yr−1, and 880.50 ± 71.72 g C m−2 yr−1 for seasonally inundated wetland; and 0.21 ± 0.1 g C m−2 yr−1, 0.28 ± 0.11 g N m−2 yr−1, and 1212.83 ± 191.98 g C m−2 yr−1 for shrub swamp. The substantial interannual variation of gas fluxes was due to the significant climatic variability which underscores the importance of long-term continuous observations. The apparent seasonal pattern of gas emissions associated with a significant relationship of gas fluxes to air temperature implied the potential effect of global warming on greenhouse gas emissions from natural wetlands. The budgets of CH4 and N2O fluxes and ecosystem respiration were highly variable among three wetland types, which suggest the uncertainties in previous studies in which all kinds of natural wetlands were treated as one or two functional types. New classification of global natural wetlands in more detailed level is highly expected.