Wetlands have been identified as the world's largest natural source of methane (CH4) and a major source of nitrous oxide (N2O) and are potential hotspots across Australia. These greenhouse gases, along with carbon dioxide (CO2), are the three most prominent atmospheric constituents contributing to current global warming. This study investigates the exchange of CH4, N2O and CO2 exchange in an Australian tropical ephemeral wetland (Fogg Dam) and the environmental factors controlling these fluxes. Wetland Net Ecosystem Production (NEP) was determined using CO2 exchange measurements using eddy covariance over 3 years. CH4 and N2O gas exchanges were measured in short campaigns during December 2006 (dry season) and February and March 2007 (wet season). The extensive coverage of vegetation in the wetland during both wet and dry seasons led to a large annual NEP (sink) of +1129.4 ± 70.4gCO2m-2yr-1 or +3.07MgCha-1y-1. Instantaneous, non-CO2 fluxes of CH4 and N2O on a CO2 equivalent basis were near zero during the dry season. However, during the wet season the CH4 source offsets approximately 93% of the CO2 sink, and N2O emission offset <1% of the CO2 sink. The primary environmental factor controlling the greenhouse gas emissions was soil water content as temperature did not vary significantly seasonally.