Carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) are key radiatively active greenhouse gases (hereafter GHGs) with variable global warming potential. Wetlands play a vital role in regulating global GHG emission through plant assimilation and soil sequestration of CO2 as well as microbial production of CH4 and N2O. These gas dynamics are greatly affected by seasonal water-level fluctuations that modulate plant productivity and dictate the location and extent of oxic and anoxic zones, which regulate soil microbial processes including denitrification and mineralization of organic carbon in detritus. Modeling results suggest that high water level lowers net CO2 emissions by promoting C storage while seasonally fluctuating water levels increased N2O production. High N-loading and high residence time of water consistently lowered net CO2 emissions but increased N2O production.