Australian ecosystems, particularly wetlands, are facing new and extreme threats due to climate change, land use, and other human interventions. However, more fundamental knowledge is required to understand how nutrient turnover in wetlands is affected. In this study, we deployed a mechanistic biogeochemical model of carbon (C), nitrogen (N), and sulfur (S) cycles at 0.25∘× 0.25∘ spatial resolution across wetlands in Australia. Our modeling was used to assess nutrient inputs to soil, elemental nutrient fluxes across the soil organic and mineral pools, and greenhouse gas (GHG) emissions in different climatic areas. In the decade 2008–2017, we estimated an average annual emission of 5.12 Tg-CH4, 90.89 Tg-CO2, and 2.34 × 10−2 Tg-N2O. Temperate wetlands in Australia have three times more N2O emissions than tropical wetlands as a result of fertilization, despite similar total area extension. Tasmania wetlands have the highest areal GHG emission rates. C fluxes in soil depend strongly on hydroclimatic factors; they are mainly controlled by anaerobic respiration in temperate and tropical regions and by aerobic respiration in arid regions. In contrast, N and S fluxes are mostly governed by plant uptake regardless of the region and season. The new knowledge from this study may help design conservation and adaptation plans to climate change and better protect the Australian wetland ecosystem.