This study investigated in-situ the seasonal and diurnal variation of emissions of greenhouse gases (GHGs) from both indigenous and exotic plant species and different environments in the Kaomei Estuary Wetland in central Taiwan with a self-designed non-dispersive infrared monitoring system. This study computed CO₂ equivalent (CO₂-e) emissions to identify their contribution to global warming. The net primary production and carbon sequestration were then estimated to determine the carbon budget of the coastal estuarine wetland. It concluded that the Kaomei Estuary Wetland functioned as a GHG source and a carbon sink. A significant diurnal variation of GHG emissions was observed, with generally lower daytime CO₂ emissions than those at nighttime, while an opposite trend was observed for CH₄ and N₂O emissions. High solar radiation in the daytime enhanced the CO₂ uptake by plant species via photosynthesis, and also accelerated the microbial activities in waters and soil/mud, both resulting in the decrease in atmospheric CO₂ concentration. The highest GHG emissions were observed in summer, followed by fall, spring, and winter. Although the concentrations of GHG emissions from the coastal estuarine wetland were in the order as CO₂>CH₄>N₂O, N₂O has the highest impact on global warming. Biomass debris played an important role in carbon sequestration, which is stored in soils and muds and stimulated methanogenic bacteria to emit CH₄. Tidal fluctuation and sewage discharge brought nitrogen-containing organics to the coastal estuarine wetland, resulting in high emission of N₂O from nitrification and denitrification processes. Two vascular plants, Spartina alterniflora, and Phragmites australis emitted more GHGs than the other two plant species. However, the highest GHG emissions from the Kaomei Estuary Wetland was attributed to Bolboschoenus planiculmis due to its largest coverage area. The annual net primary production (NPP) varied mainly with vegetation coverage and season. The exotic Spartina alterniflora had the highest annual NPP compared to the indigenous plant species because of its high nutrient uptake from the soil/mud by its thriving roots.