Our understanding of tree stem methane (CH4) emissions is evolving rapidly. Few studies have combined seasonal measurements of soil, water and tree stem CH4 emissions from forested wetlands, inhibiting our capacity to constrain the tree stem CH4 flux contribution to total wetland CH4 flux. Here we present annual data from a subtropical freshwater Melaleuca quinquenervia wetland forest, spanning an elevational topo-gradient (Lower, Transitional and Upper zones). Eight field-campaigns captured an annual hydrological flood-dry-flood cycle, measuring stem fluxes on 30 trees, from four stem heights, and up to 30 adjacent soil or water CH4 fluxes per campaign. Tree stem CH4 fluxes ranged several orders of magnitude between hydrological seasons and topo-gradient zones, spanning from small CH4 uptake to ~203 mmol m-2 d-1. Soil CH4 fluxes were similarly dynamic and shifted from maximal CH4 emission (saturated soil) to uptake (dry soil). In Lower and Transitional zones respectively, tree stem CH4 contribution to the net ecosystem flux was greatest during flooded conditions (49.9 and 70.2 %) but less important during dry periods (3.1 and 28.2 %). Minor tree stem emissions from the Upper elevation zone still offset the Upper zone CH4 soil sink capacity by ~51% during dry conditions. Water table height was the strongest driver of tree stem CH4 fluxes, however tree emissions peaked once the soil was inundated and did not increase with further water depth. This study highlights the importance of quantifying the wetland tree stem CH4 emissions pathway as an important and seasonally oscillating component of wetland CH4 budgets.