Research surrounding tree stem methane (CH4) emissions is rapidly growing. Long-term and seasonal studies are rare but essential to constrain large spatial and seasonal emissions variability, and to resolve the tree stem contribution to the total wetland methane flux i.e. soil, water and trees. Here we present annual methane emissions data from a subtropical freshwater Melaleuca quinquenervia wetland forest. We measured methane emissions in situ along a ~3 m topo-gradient, encompassing forest in lower, transitional and upper elevation zones. Nine field campaigns at ~6 weekly intervals, captured a flood-dry-flood annual hydrological cycle (max. water depth 305 cm). We measured stem fluxes from 30 trees at four stem heights (40, 70, 100, 130 cm) and 30 adjacent soil or water CH4 fluxes per campaign. Tree stem methane fluxes ranged several orders of magnitude between hydrological seasons and topo-gradient zones (ranging from uptake to 1595 mmol m-2 tree-stem d-1). Soil fluxes were similar in amplitude and shifted from maximal CH4 emissions during the wettest conditions, to CH4 uptake under dry soil conditions. The importance of tree stem emissions to net ecosystem flux (NEF) was most substantial during flooded conditions, ranging from 37-59% NEF in the lower and transitional zones respectively. In the upper zone, the tree stem emissions offset the upland soil sink capacity by ~10%. This study shows the importance of quantifying wetland tree stem CH4 emissions pathway as a substantial contributor to the total wetland flux. This data also provides important baseline readings for the southern hemisphere and Australian wetland forests, which generally experience dynamic rainfall and soil redox oscillations between flooding and droughts.